Re: [PyMOL] How to color in a different way different helix types?

[H. Adam Steinberg]

Hi Ramiro,

Like you, I would love to see secondary structure colored by helix type.  Jmol 
however does not show this as a default. Do you know what steps you took to get 
Jmol to show secondary structure colored by helix type?

I can't seem to find that setting in any of the menu options.

style/scheme/cartoon
color/structure/cartoon/By Scheme/Secondary Structure

This shows all of the helices in the same color.

Adam


On Apr 6, 2011, at 4:22 AM, Ramiro Téllez Sanz wrote:

> Hi and thanks for reading this.
> 
> I have googled for a way to achieve what I want and have gone through
> the wiki, to no avail.
> 
> I would like to color in a different way the different helix types:
> alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get
> distinct colors for each type by default. But if the same pdb file is
> open with PyMOL all helices are treated the same way. Can't PyMOL
> distinguish helix types?
> 
> Thanks in advance,
> Ramiro Téllez Sanz
> Dept. Physical Chemistry
> University of Almeria
> Spain
> 
> --
> Xperia(TM) PLAY
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> smartphone on the nation's most reliable network.
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H. Adam Steinberg
Artist, Scientist, Developmental Editor

www.artforscience.com
7904 Bowman Rd
Lodi, WI 53555
608/729-5944


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Re: [PyMOL] How to color in a different way different helix types?

[H. Adam Steinberg]

Jason (or someone else),

Is there way in pymol to look for the following angle in a structure φ=-49o and 
ψ=-26o ? Which is the definition of a 310 helix. And yes we'd have to search 
for a few degrees plus of minus of those angles. They should all appear in 
tight turns and last for about 3 or 4 amino acids (I don't think there wouldn't 
be any cartoon helix shown).

I don't think there are any pdbs yet that contain pi helices (because of the 
loose packing and steric hindrance of the side chains), does anyone know of any?

Thanks 

Adam

On Apr 6, 2011, at 8:16 AM, Jason Vertrees wrote:

> Hi Ramiro,
> 
> PyMOL doesn't differentiate helices, so it cannot color them
> differently.  If you had the residue labels from some other program
> you could read them in and then color by type.
> 
> Cheers,
> 
> -- Jason
> 
> On Wed, Apr 6, 2011 at 5:22 AM, Ramiro Téllez Sanz  
> wrote:
>> Hi and thanks for reading this.
>> 
>> I have googled for a way to achieve what I want and have gone through
>> the wiki, to no avail.
>> 
>> I would like to color in a different way the different helix types:
>> alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get
>> distinct colors for each type by default. But if the same pdb file is
>> open with PyMOL all helices are treated the same way. Can't PyMOL
>> distinguish helix types?
>> 
>> Thanks in advance,
>> Ramiro Téllez Sanz
>> Dept. Physical Chemistry
>> University of Almeria
>> Spain
>> 
>> --
>> Xperia(TM) PLAY
>> It's a major breakthrough. An authentic gaming
>> smartphone on the nation's most reliable network.
>> And it wants your games.
>> http://p.sf.net/sfu/verizon-sfdev
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> 
> 
> 
> 
> -- 
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
> 
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
> 
> --
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> smartphone on the nation's most reliable network.
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[PyMOL] bbPlane script "SyntaxError: invalid syntax"

[H. Adam Steinberg]

Hi all,

Can anyone help me with a problem that I am having trying to run a python 
script?
I am trying to run the bbPlane script from the PyMOLWiki 
<http://www.pymolwiki.org/index.php/BbPlane>
I have copied the script from the web page, to a plain text document, saved it 
as "bbPlane.py" but when I run it I get:


PyMOL>run bbPlane.py
Traceback (most recent call last):
  File "/Volumes/Port 3/software/MacPyMOL.app/pymol/modules/pymol/parser.py", 
line 332, in parse
  File "/Volumes/Port 3/software/MacPyMOL.app/pymol/modules/pymol/parsing.py", 
line 455, in run_file
  File "bbPlane.py", line 14
 
 ^
 SyntaxError: invalid syntax 
-

script is here:
#
# -- bbPlane.py - draws a CGO plane across the backbone atoms of
# neighboring amino acids
# 
# Author: Jason Vertrees, 06/2010
#   Modified by Thomas Holder, 06/2010
#   Modified by Blaine Bell, 08/2011
# Copyright (C) Schrodinger
# Open Source License: MIT
#
from pymol.cgo import *# get constants
from pymol import cmd, stored
from chempy import cpv
 
def bbPlane(objSel='(all)', color='white', transp=0.0):
"""
DESCRIPTION
 
Draws a plane across the backbone for a selection
 
ARGUMENTS
 
objSel = string: protein object or selection {default: (all)}
 
color = string: color name or number {default: white}
 
transp = float: transparency component (0.0--1.0) {default: 0.0}
 
NOTES
 
You need to pass in an object or selection with at least two
amino acids.  The plane spans CA_i, O_i, N-H_(i+1), and CA_(i+1)
"""
# format input
transp = float(transp)
stored.AAs = []
coords = dict()
 
# need hydrogens on peptide nitrogen
cmd.h_add('(%s) and n. N' % objSel)
 
# get the list of residue ids
for obj in cmd.get_object_list(objSel):
sel = obj + " and (" + objSel + ")"
for a in cmd.get_model(sel + " and n. CA").atom:
key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
stored.AAs.append(key)
coords[key] = [a.coord,None,None]
for a in cmd.get_model(sel + " and n. O").atom:
key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
if key in coords:
coords[key][1] = a.coord
for a in cmd.get_model("(hydro or n. CD) and nbr. (" + sel + " and n. 
N)").atom:
key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
if key in coords:
coords[key][2] = a.coord
 
# need at least two amino acids
if len(stored.AAs) <= 1:
print "ERROR: Please provide at least two amino acids, the alpha-carbon 
on the 2nd is needed."
return
 
# prepare the cgo
obj = [
BEGIN, TRIANGLES,
COLOR,
]
obj.extend(cmd.get_color_tuple(color))
 
for res in range(0, len(stored.AAs)-1):
curIdx, nextIdx = str(stored.AAs[res]), str(stored.AAs[res+1])
 
# populate the position array
pos = [coords[curIdx][0], coords[curIdx][1], coords[nextIdx][2], 
coords[nextIdx][0]]
 
# if the data are incomplete for any residues, ignore
if None in pos:
print 'peptide bond %s -> %s incomplete' % (curIdx, nextIdx)
continue
 
if cpv.distance(pos[0], pos[3]) > 4.0:
print '%s and %s not adjacent' % (curIdx, nextIdx)
continue
 
# need to order vertices to generate correct triangles for plane
#  modified/added by B.Bell 8/18/2011
sumpos = cpv.add(pos[0], cpv.add(pos[1], cpv.add(pos[2], pos[3])))
centerpos = [ sumpos[0]/4., sumpos[1]/4., sumpos[2]/4. ]
angles = [ [ 0., 0 ] ]
s00 = cpv.sub(pos[0], centerpos)
for i in range(1,4):
s = cpv.sub(pos[i], centerpos)
ang = cpv.get_angle(s00, s)
angles.append( [ ang, i] )
def sortfirst(a, b):
return cmp(a[0], b[0])
angles.sort(sortfirst)
verts = map(lambda x: x[1], angles)
vorder = [ verts[0], verts[1], verts[2],
   verts[1], verts[3], verts[2] ]
# fill in the vertex data for the triangles; 
for i in vorder:
obj.append(VERTEX)
obj.extend(pos[i])
 
# finish the CGO
obj.append(END)
 
# update the UI
newName =  cmd.get_unused_name("backbonePlane")
cmd.load_cgo(obj, newName)
cmd.set("cgo_transparency", transp, newName)
 
 
cmd.extend("bbPlane", bbPlane)


artforscience

H. Adam Steinberg
Artist, Scientist, Developmental Editor

www.artforscience.com
7904 Bowman Rd
Lodi, WI 53555
608/729-5944

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Re: [PyMOL] bbPlane script "SyntaxError: invalid syntax"

[H. Adam Steinberg]

I erased all of the spaces in the "blank" lines and now the script works. When 
I erased them in line 14 then it found them in kine 38, etc. You may want to 
update the script on the WIki to one without spaces.

I am trying to follow the example in the Wiki to make sure it works before I 
try it on my pdb. However, when I run the command "bbPlane i. 4-10" I get a new 
error:

PyMOL>bbPlane i. 4-10
Traceback (most recent call last):
  File "/Volumes/Port 3/software/MacPyMOL.app/pymol/modules/pymol/parser.py", 
line 250, in parse
  File "bbPlane.py", line 110, in bbPlane
newName =  cmd.get_unused_name("backbonePlane")
AttributeError: 'module' object has no attribute 'get_unused_name'

On Aug 25, 2011, at 11:09 AM, Jason Vertrees wrote:

> Hi Adam,
> 
> I just copy/pasted the script you attached in your email and it worked
> fine. There are, however two spaces on line 14--maybe the parser
> thinks it found a block indent? Try erasing line 14 (the line
> following "from chempy import cpv") and re-running the script.
> 
> Cheers,
> 
> -- Jason
> 
> On Thu, Aug 25, 2011 at 11:34 AM, H. Adam Steinberg  
> wrote:
>> Hi all,
>> Can anyone help me with a problem that I am having trying to run a python
>> script?
>> I am trying to run the bbPlane script from the PyMOLWiki
>> <http://www.pymolwiki.org/index.php/BbPlane>
>> I have copied the script from the web page, to a plain text document, saved
>> it as "bbPlane.py" but when I run it I get:
>> 
>> PyMOL>run bbPlane.py
>> Traceback (most recent call last):
>>   File "/Volumes/Port
>> 3/software/MacPyMOL.app/pymol/modules/pymol/parser.py", line 332, in parse
>>   File "/Volumes/Port
>> 3/software/MacPyMOL.app/pymol/modules/pymol/parsing.py", line 455, in
>> run_file
>>   File "bbPlane.py", line 14
>> 
>>  ^
>>  SyntaxError: invalid syntax
>> -
>> script is here:
>> 
>> #
>> # -- bbPlane.py - draws a CGO plane across the backbone atoms of
>> # neighboring amino acids
>> #
>> # Author: Jason Vertrees, 06/2010
>> #   Modified by Thomas Holder, 06/2010
>> #   Modified by Blaine Bell, 08/2011
>> # Copyright (C) Schrodinger
>> # Open Source License: MIT
>> #
>> from pymol.cgo import *# get constants
>> from pymol import cmd, stored
>> from chempy import cpv
>> 
>> def bbPlane(objSel='(all)', color='white', transp=0.0):
>>"""
>> DESCRIPTION
>> 
>>Draws a plane across the backbone for a selection
>> 
>> ARGUMENTS
>> 
>>objSel = string: protein object or selection {default: (all)}
>> 
>>color = string: color name or number {default: white}
>> 
>>transp = float: transparency component (0.0--1.0) {default: 0.0}
>> 
>> NOTES
>> 
>>You need to pass in an object or selection with at least two
>>amino acids.  The plane spans CA_i, O_i, N-H_(i+1), and CA_(i+1)
>>"""
>># format input
>>transp = float(transp)
>>stored.AAs = []
>>coords = dict()
>> 
>># need hydrogens on peptide nitrogen
>>cmd.h_add('(%s) and n. N' % objSel)
>> 
>># get the list of residue ids
>>for obj in cmd.get_object_list(objSel):
>>sel = obj + " and (" + objSel + ")"
>>for a in cmd.get_model(sel + " and n. CA").atom:
>>key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>>stored.AAs.append(key)
>>coords[key] = [a.coord,None,None]
>>for a in cmd.get_model(sel + " and n. O").atom:
>>key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>>if key in coords:
>>coords[key][1] = a.coord
>>for a in cmd.get_model("(hydro or n. CD) and nbr. (" + sel + " and
>> n. N)").atom:
>>key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>>if key in coords:
>>coords[key][2] = a.coord
>> 
>># need at least two amino acids
>>if len(stored.AAs) <= 1:
>>print "ERROR: Please provide at least two amino acids, the
>> alpha-carbon on the 2nd is needed."
>>return
>> 
>># prepare the cgo
>>obj = [
>>BEGIN, TRIANGLES,
>>COLOR,
>>]
>>obj.extend(cmd.get_col

Re: [PyMOL] bbPlane script "SyntaxError: invalid syntax"

[H. Adam Steinberg]

Thanks Tsjerk,

When I run this script, I see:

PyMOL>pplanes selection, (sele)
Selector-Error: Invalid Selection Name.
( selection and n. ca )<-- 

I have tried selecting just one "n and ca" in the pdb, tried selecting multiple 
"n and ca", tried a bunch of other selections, but it's not working. What am I 
supposed to be selecting in the pdb to make the script work?


On Aug 25, 2011, at 11:28 AM, Tsjerk Wassenaar wrote:

> Hi Adam,
> 
> Here's an alternative script... The command is pplanes (peptide-planes):
> 
> run triangles.py
> pplanes selection[, color[, alpha[, state[, name
> 
> Hope it helps,
> 
> Tsjerk
> 
> 
> On Thu, Aug 25, 2011 at 5:34 PM, H. Adam Steinberg  wrote:
>> Hi all,
>> Can anyone help me with a problem that I am having trying to run a python
>> script?
>> I am trying to run the bbPlane script from the PyMOLWiki
>> <http://www.pymolwiki.org/index.php/BbPlane>
>> I have copied the script from the web page, to a plain text document, saved
>> it as "bbPlane.py" but when I run it I get:
>> 
>> PyMOL>run bbPlane.py
>> Traceback (most recent call last):
>>   File "/Volumes/Port
>> 3/software/MacPyMOL.app/pymol/modules/pymol/parser.py", line 332, in parse
>>   File "/Volumes/Port
>> 3/software/MacPyMOL.app/pymol/modules/pymol/parsing.py", line 455, in
>> run_file
>>   File "bbPlane.py", line 14
>> 
>>  ^
>>  SyntaxError: invalid syntax
>> -
>> script is here:
>> 
>> #
>> # -- bbPlane.py - draws a CGO plane across the backbone atoms of
>> # neighboring amino acids
>> #
>> # Author: Jason Vertrees, 06/2010
>> #   Modified by Thomas Holder, 06/2010
>> #   Modified by Blaine Bell, 08/2011
>> # Copyright (C) Schrodinger
>> # Open Source License: MIT
>> #
>> from pymol.cgo import *# get constants
>> from pymol import cmd, stored
>> from chempy import cpv
>> 
>> def bbPlane(objSel='(all)', color='white', transp=0.0):
>>"""
>> DESCRIPTION
>> 
>>Draws a plane across the backbone for a selection
>> 
>> ARGUMENTS
>> 
>>objSel = string: protein object or selection {default: (all)}
>> 
>>color = string: color name or number {default: white}
>> 
>>transp = float: transparency component (0.0--1.0) {default: 0.0}
>> 
>> NOTES
>> 
>>You need to pass in an object or selection with at least two
>>amino acids.  The plane spans CA_i, O_i, N-H_(i+1), and CA_(i+1)
>>"""
>># format input
>>transp = float(transp)
>>stored.AAs = []
>>coords = dict()
>> 
>># need hydrogens on peptide nitrogen
>>cmd.h_add('(%s) and n. N' % objSel)
>> 
>># get the list of residue ids
>>for obj in cmd.get_object_list(objSel):
>>sel = obj + " and (" + objSel + ")"
>>for a in cmd.get_model(sel + " and n. CA").atom:
>>key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>>stored.AAs.append(key)
>>coords[key] = [a.coord,None,None]
>>for a in cmd.get_model(sel + " and n. O").atom:
>>key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>>if key in coords:
>>coords[key][1] = a.coord
>>for a in cmd.get_model("(hydro or n. CD) and nbr. (" + sel + " and
>> n. N)").atom:
>>key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>>if key in coords:
>>coords[key][2] = a.coord
>> 
>># need at least two amino acids
>>if len(stored.AAs) <= 1:
>>print "ERROR: Please provide at least two amino acids, the
>> alpha-carbon on the 2nd is needed."
>>return
>> 
>># prepare the cgo
>>obj = [
>>BEGIN, TRIANGLES,
>>COLOR,
>>]
>>obj.extend(cmd.get_color_tuple(color))
>> 
>>for res in range(0, len(stored.AAs)-1):
>>curIdx, nextIdx = str(stored.AAs[res]), str(stored.AAs[res+1])
>> 
>># populate the position array
>>pos = [coords[curIdx][0], coords[curIdx][1], coords[nextIdx][2],
>> coords[nextIdx][0]]
>> 
>># if the data are incomplete for any residues, ignore
>>if None in pos:
>>print 'peptide bond 

[PyMOL] pdb of ice

[H. Adam Steinberg]

Hi all,

Does anyone know of a pdb that was created for the structure of water molecules 
in ice? I have not been able to find one and am not looking forward to creating 
one! :)

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


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Re: [PyMOL] pdb of ice

[H. Adam Steinberg]

Thank you Joel!

DOH! let this be a lesson on keeping searches simple... if you want a pdb for 
ice simply search for "ice .pdb"! forget about using words like molecular, 
dynamics, structure, crystal, etc. :)

Adam

On Oct 20, 2011, at 8:31 PM, Joel Tyndall wrote:

> A quick google search found this:
> 
> http://www.nyu.edu/pages/mathmol/library/water/ 
> 
> hope this helps
> 
> _
> Joel Tyndall, PhD
> 
> Senior Lecturer in Medicinal Chemistry
> National School of Pharmacy
> University of Otago
> PO Box 56 Dunedin 9054
> New Zealand   
> Skype: jtyndall
> http://www.researcherid.com/rid/C-2803-2008
> Pukeka Matua
> Te Kura Taiwhanga Putaiao
> Te Whare Wananga o Otago
> Pouaka Poutapeta 56 Otepoti 9054
> Aotearoa
> 
> Ph / Waea   +64 3 4797293
> Fax / Waeawhakaahua +64 3 4797034
> 
> 
> -Original Message-
> From: H. Adam Steinberg [mailto:a...@steinbergs.us] 
> Sent: Friday, 21 October 2011 9:31 a.m.
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] pdb of ice
> 
> Hi all,
> 
> Does anyone know of a pdb that was created for the structure of water 
> molecules in ice? I have not been able to find one and am not looking forward 
> to creating one! :)
> 
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
> 
> 
> --
> The demand for IT networking professionals continues to grow, and the demand 
> for specialized networking skills is growing even more rapidly.
> Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco 
> certifications, training, and career opportunities. 
> http://p.sf.net/sfu/cisco-dev2dev
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


--
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demand for specialized networking skills is growing even more rapidly.
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[PyMOL] cartoon from c-alphas JMol vs PyMol

[H. Adam Steinberg]

Hi all,

If you open a c-alpha pdb (3ixz for example) in PyMol, you can show the 
c-alphas as spheres, or you can show a cartoon as a tube (ribbon like) but you 
can make a traditional flat faced PyMol cartoon. Yet when you open the same pdb 
in JMol it shows the traditional PyMol cartoon as the default. :P

Why can't PyMol show the traditional cartoon like JMol does? and if JMol is 
faking the traditional cartoon, why can't we get PyMol to also fake the 
traditional cartoon? :)

Thanks for any insight.

Adam

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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[PyMOL] Structural biologist job

[H. Adam Steinberg]

Hi all,

A friend of mine is looking to hire a structural biologist. With the tight job 
market I though I would try and get this out to as many people as possible.


> I am looking to hire a PhD structural biologist to join the team I manage at 
> Myriad Genetic Laboratories in Salt Lake City, Utah. Please 
> forward/post/pin-up the attached pdf if you can think of anybody who might be 
> interested, or if you can think of someone that might know someone who might 
> be interested. 
> 
> Myriad Genetics is a great company to work for, with all the perks of a 
> biotech company (employee stock option purchase plan, 401k company match, 
> full benefits, etc). Myriad Genetics is nestled in the foothills of the Rocky 
> Mountains with over 1,100 employees and growing. Salt Lake City is a great 
> place to live both for the outdoorsy person, as well as the cultural arts 
> type person. It’s also a great place to raise a family.
> 
> Please email all job inquiries to Dr. Julie Eggington at 
> .
> 
> Thank you.
> Julie
> 
> Myriad Genetics - Clinical Variant Specialist unofficial job posting 2012.pdf 

 JOB OPENING:  Clinical Variant Specialist
Requires Ph.D. in Biochemistry or related field, with emphasis in structural 
biology.  

Location: Myriad Genetic Laboratories, Inc. Salt Lake City, UT. Full time 
position NOTE: This is an early, unofficial job posting.  Official job postings 
are found at www.myriad.com  

Overview: Myriad Genetic Laboratories is a leading molecular diagnostic company 
based in Salt Lake City, Utah. Myriad offers predictive medicine tests that 
identify hereditary breast and ovarian cancer, hereditary colorectal and 
uterine cancer, and other hereditary cancer syndromes. DNA sequencing allows 
Myriad to detect these syndromes by identifying disease causing mutations in 
specific genes. However, not all genetic variants which are identified in DNA 
testing are disease causing. Initially, some variants are classified as 
"Genetic Variant of Uncertain Significance" until research shows whether or not 
the genetic variant is disease causing or benign. It is the role of Myriad's 
Variant Specialist Team to collect and analyze data so that these Genetic 
Variants of Uncertain Significance can be correctly classified in a clinical 
setting.

  The Variant Specialist Team is looking to hire an expert in structural 
biology.  Unlike traditional Scientist I/II positions in biotechnology, the 
Clinical Variant Specialist is not likely to pursue lab bench work, but will 
apply his/her skills to reviewing literature and using molecular modeling and 
bio‐informatics approaches to assist in better understanding the effects of 
genetic mutations.  The Clinical Variant Specialist will work within a larger 
group of cross‐disciplinary scientists and statisticians.  Additionally, the 
Clinical Variant Specialist will work with clinician customers to assist in 
scientific understanding and in the coordination of research studies.  
Excellent communication skills are required.  Attendance at professional 
meetings and publication opportunities are fostered.  The clinical Variant 
Specialist will also work on a variety of projects across different non‐science 
divisions within Myriad as a representative of the Variant Specialist Team. 

Qualifications:
‐Ph.D. in Biochemistry or a related field required, with emphasis in structural 
biology 
‐Excellent written and verbal communication skills 
‐Candidates with postdoctoral research experience or equivalent are preferred 
‐Candidates with experience in protein‐nucleic acid interactions and/or 
experience in cancer causing biological pathways are preferred  

How to apply: ‐Applications are to be formally made through 
http://www.myriad.com/careers/ when the position officially posts (likely in 
July 2012).  The position may have a different title at time of posting.  Dr. 
Julie Eggington is seeking resumes early to screen candidates as soon as 
possible starting in June 2012.  To facilitate this, please email resumes and 
enquiries to Dr. Julie Eggington at jeggi...@myriad.com with “Clinical Variant 
Specialist Job Opening” in the subject line.  

About Myriad:  Myriad Genetics, Inc. (Nasdaq: MYGN) is a leading molecular 
diagnostic company dedicated to making a difference in patient’s lives through 
the discovery and commercialization of transformative tests to assess a 
person’s risk of developing disease, guide treatment decisions and assess risk 
of disease progression and recurrence.  With fiscal year 2011 revenue of over 
$400 million and more than 1,100 employees, Myriad is working on strategic 
directives, including new test introductions, companion diagnostics, and 
international expansion, to take advantage of significant growth opportunities 
to further the Company’s mission. Thanks to the dedication of our employees, 
the Company is succeeding in making a difference by improving the quality of 
patient’s lives and saving lives.  For more informatio

Re: [PyMOL] PyMOLWiki is Down

[H. Adam Steinberg]

Is the wiki still in turmoil? every time I try to access a page via the search 
field on the wiki, or via a Google search I get back "connection reset" in 
Firefox and "server dropped the connection" in Safari.

I need the wiki! :)


On Jun 12, 2012, at 8:42 AM, Jason Vertrees wrote:

> Greetings,
> 
> The PyMOLWiki recently went down due to a vulnerability in MySQL. If
> we cannot repair the system over the next day or so, we'll put up a
> mirror from the last backup (about 9 days ago) on a system without the
> vulnerability.
> 
> Google has very thoroughly cached the PyMOLWiki, so in the meantime,
> you should still be able to search and find what you need -- and dont'
> forget you can always email this list.
> 
> Cheers,
> 
> -- Jason
> 
> -- 
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrödinger, LLC
> 
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
> 
> --
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> ___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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H. Adam Steinberg
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608/592-2366


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Re: [PyMOL] PyMOLWiki is Down

[H. Adam Steinberg]

I just tried it again and it does indeed work. But over the last few weeks (on 
first attempts) it seems to return an error. Maybe it's just my satellite ISP...

Thanks

On Jul 5, 2012, at 3:21 PM, Jason Vertrees wrote:

> Hi Adam,
> 
> The PyMOLWiki is working fine from here. Anyone else having problems?
> 
> Cheers,
> 
> -- Jason
> 
> On Thu, Jul 5, 2012 at 3:04 PM, H. Adam Steinberg  wrote:
>> Is the wiki still in turmoil? every time I try to access a page via the 
>> search field on the wiki, or via a Google search I get back "connection 
>> reset" in Firefox and "server dropped the connection" in Safari.
>> 
>> I need the wiki! :)
>> 
>> 
>> On Jun 12, 2012, at 8:42 AM, Jason Vertrees wrote:
>> 
>>> Greetings,
>>> 
>>> The PyMOLWiki recently went down due to a vulnerability in MySQL. If
>>> we cannot repair the system over the next day or so, we'll put up a
>>> mirror from the last backup (about 9 days ago) on a system without the
>>> vulnerability.
>>> 
>>> Google has very thoroughly cached the PyMOLWiki, so in the meantime,
>>> you should still be able to search and find what you need -- and dont'
>>> forget you can always email this list.
>>> 
>>> Cheers,
>>> 
>>> -- Jason
>>> 
>>> --
>>> Jason Vertrees, PhD
>>> PyMOL Product Manager
>>> Schrödinger, LLC
>>> 
>>> (e) jason.vertr...@schrodinger.com
>>> (o) +1 (603) 374-7120
>>> 
>>> --
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and
>>> threat landscape has changed and how IT managers can respond. Discussions
>>> will include endpoint security, mobile security and the latest in malware
>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>> ___
>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366
>> 
> 
> 
> 
> -- 
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrödinger, LLC
> 
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


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[PyMOL] MacPyMOL 1.4 vs 1.5 problem with color

[H. Adam Steinberg]

Hi all,

If you run the script below to get a nice blob type surface (great for 
illustrations) in 1.4 it all works perfectly, and you can color the new map 
surface any color you want.
If you run the same script in 1.5 it all works perfectly too, but no matter 
what you do you cannot change the color of the new map surface from the default 
white to any other color. Not via the settings, the command line, nor the gui 
menus.

Is there a command I can add to the script below that will allow me to change 
the color of map surface (surfA)? or are there new commands that I should use 
in this script to make this work in 1.5? or is this now broken in 1.5.0.4?

---
set surface_quality, 1
alter all, b=50
alter all, q=1
set gaussian_resolution,5
map_new mapA, gaussian, 1, sele or pdb, 6
isosurface surfA, mapA
-

Thanks in advance for the help!


H. Adam Steinberg
7904 Bowman Rd
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608/592-2366


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Re: [PyMOL] MacPyMOL 1.4 vs 1.5 problem with color

[H. Adam Steinberg]

Thanks Thomas, that does work.

On Nov 23, 2012, at 6:31 AM, Thomas Holder wrote:

> Hi Adam,
> 
> this seems to be not yet fully implemented with the new shader
> rendering. So you may turn shaders off for now:
> 
> PyMOL> unset use_shaders
> 
> Ray tracing is not affected, so you still can generate high quality
> figures with correct colors:
> 
> PyMOL> ray
> 
> Hope that helps.
> 
> Cheers,
>  Thomas
> 
> H. Adam Steinberg wrote, On 11/20/12 03:40:
>> Hi all,
>> 
>> If you run the script below to get a nice blob type surface (great for 
>> illustrations) in 1.4 it all works perfectly, and you can color the new map 
>> surface any color you want.
>> If you run the same script in 1.5 it all works perfectly too, but no matter 
>> what you do you cannot change the color of the new map surface from the 
>> default white to any other color. Not via the settings, the command line, 
>> nor the gui menus.
>> 
>> Is there a command I can add to the script below that will allow me to 
>> change the color of map surface (surfA)? or are there new commands that I 
>> should use in this script to make this work in 1.5? or is this now broken in 
>> 1.5.0.4?
>> 
>> ---
>> set surface_quality, 1
>> alter all, b=50
>> alter all, q=1
>> set gaussian_resolution,5
>> map_new mapA, gaussian, 1, sele or pdb, 6
>> isosurface surfA, mapA
>> -
>> 
>> Thanks in advance for the help!
>> 
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366
> 
> -- 
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
> 
> --
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[PyMOL] default settings

[H. Adam Steinberg]

Hi All,

PyMol has it's own default settings, many of them are the historically accepted 
ways to view structures, universally accepted colors, etc. and that is great, 
because when someone uses the program they have to start with something! :)

And I realize most users probably open a pdb, work on, close the program, and 
then don't use it again for days or weeks. However, once someone uses the 
program all day long, day after day after day, once someone moves beyond the 
basics, develops a unique color set, develops a new style, develops a better 
style, or is working on a project that requires dozens, or even hundreds of 
renderings that all need to based on defaults that are different from the 
original defaults the program has built in, it gets to be quite a pain to have 
to run a default script every time one loads another pdb to a working open 
window, or when one opens another running window of PyMol.

Is there anyway to change the default settings in PyMol so that when I open the 
program, it is using my specified defaults? or perhaps there is a way a script 
can automatically be run at startup? Or automatically run when I fetch in a new 
pdb? I'm running MacPyMol on 10.8.

Thanks

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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Re: [PyMOL] default settings

[H. Adam Steinberg]

This is great, but looks like it's only for Windows? Where would one put this 
pymolrc.pym file on a Mac?

<http://www.pymolwiki.org/index.php/Pymolrc>

On Jan 30, 2013, at 12:12 PM, Nat Echols  wrote:

> On Wed, Jan 30, 2013 at 8:33 AM, H. Adam Steinberg  wrote:
>> Is there anyway to change the default settings in PyMol so that when I open
>> the program, it is using my specified defaults? or perhaps there is a way a
>> script can automatically be run at startup? Or automatically run when I
>> fetch in a new pdb? I'm running MacPyMol on 10.8.
> 
> Yes, just create a file ~/.pymolrc and add whatever settings you want
> - for instance, this is mine:
> 
> set auto_zoom = 0
> set cartoon_oval_length = 0.8
> set cartoon_oval_width = 0.15
> set cartoon_rect_length = 0.8
> set cartoon_rect_width = 0.15
> set ray_shadows = 0
> set ray_opaque_background = 0
> 
> -Nat

H. Adam Steinberg
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608/592-2366


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Re: [PyMOL] default settings

[H. Adam Steinberg]

You are correct, if I put the pymolrc.pym file in the user folder, MacPyMol 
does try to read it when it starts up.

However, it errors every time.

If I put just this one command in the file and start up PyMol, it comes back 
with:

 File "/Users/adam/pymolrc.pym", line 1
set auto_zoom = 0
^
SyntaxError: invalid syntax

On Jan 30, 2013, at 12:46 PM, Nat Echols  wrote:

> On Wed, Jan 30, 2013 at 10:43 AM, H. Adam Steinberg  
> wrote:
>> This is great, but looks like it's only for Windows? Where would one put 
>> this pymolrc.pym file on a Mac?
>> 
>> <http://www.pymolwiki.org/index.php/Pymolrc>
> 
> Quoting the wiki:
> 
> "On a linux-type system, this file will be located in /path/to/home/.pymolrc."
> 
> This should probably be edited to "Unix-type system", since Mac and
> Linux behave identically in this case.
> 
> -Nat

H. Adam Steinberg
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Lodi, WI 53555
608/592-2366


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Re: [PyMOL] default settings

[H. Adam Steinberg]

1st, thank you for your patience and help.
2nd, for those who end up trying to also do this… Apple now hides all files in 
the user folder that start with a period. Therefore, the minute you hit enter 
after changing the name to .pymolrc, the file disappears. You have to run a 
third party app that allows you to see the hidden files. I used TinkerTool.

This works and solved the problem! Thanks!


On Jan 30, 2013, at 12:59 PM, Nat Echols  wrote:

> On Wed, Jan 30, 2013 at 10:56 AM, H. Adam Steinberg  
> wrote:
>> You are correct, if I put the pymolrc.pym file in the user folder, MacPyMol 
>> does try to read it when it starts up.
>> 
>> However, it errors every time.
>> 
>> If I put just this one command in the file and start up PyMol, it comes back 
>> with:
>> 
>> File "/Users/adam/pymolrc.pym", line 1
>>set auto_zoom = 0
>>^
>> SyntaxError: invalid syntax
> 
> That's because you're using the wrong file name:
> 
>>> "On a linux-type system, this file will be located in 
>>> /path/to/home/.pymolrc."
> 
> 
> -Nat

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608/592-2366


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[PyMOL] Leap motion control

[H. Adam Steinberg]

It would be great if we could control PyMOL with a Leap Motion control 
<https://www.leapmotion.com>.

I see it supports molecules.

H. Adam Steinberg
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608/592-2366


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Re: [PyMOL] set line_width command doesn't work

[H. Adam Steinberg]

You just have to Ray the figure to see the changes.


On Sep 4, 2013, at 10:21 AM, "sunyeping"  wrote:

> Dear all
>  
> I want to make line presentation in pymol looks more thicker so I enter "set 
> line_width, 3", but the lines in the viewer window don't show any change. 
> Have you meet such circumstance? The pymol (version 1.5.0.1) is installed in 
> centos5.9 system and other functions seem well. Thanks.
>  
> Yeping Sun
> 
> Institute of Microbiology, Chinese Academy of Sciences
> 

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Re: [PyMOL] Molecular models with LEGO

[H. Adam Steinberg]

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[PyMOL] Sphere_scale vs Dot_scale

[H. Adam Steinberg]

I can show an atom as a sphere, and then scale that sphere to 0.5.
I can show an atom as dots, but then cannot scale the volume of those “dots” to 
0.5. There is no dot_scale command in PyMOL.

Is there anyway to scale the volume of the dots in some way?


H. Adam Steinberg
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608/592-2366

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Re: [PyMOL] Sphere_scale vs Dot_scale

[H. Adam Steinberg]

Works perfectly! Thank you so much!

On Dec 9, 2013, at 2:43 PM, Thomas Holder  wrote:

> Hi Adam,
> 
> alter all, vdw*=0.5
> rebuild
> 
> Cheers,
>  Thomas
> 
> On 09 Dec 2013, at 14:51, H. Adam Steinberg  
> wrote:
> 
>> I can show an atom as a sphere, and then scale that sphere to 0.5.
>> I can show an atom as dots, but then cannot scale the volume of those “dots” 
>> to 0.5. There is no dot_scale command in PyMOL.
>> 
>> Is there anyway to scale the volume of the dots in some way?
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366

H. Adam Steinberg
7904 Bowman Rd
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608/592-2366


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[PyMOL] filled rings

[H. Adam Steinberg]

Hi All,

Somehow I have turned on or adjusted a setting and cannot figure out what it is 
or how to turn it off.

All of the rings in my nucleic acid structures are filled (and that is okay) 
but they are all filled with green! They are not filled with the same color as 
the rest of the base.

Can anyone help?

Sample image attached…



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Re: [PyMOL] filled rings

[H. Adam Steinberg]

THANK YOU, that was it!

On Jun 16, 2014, at 5:22 PM, Sampson, Jared  wrote:

> set cartoon_ring_color, blue, my_selection

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Re: [PyMOL] Cartoon_oval_length

[H. Adam Steinberg]

1) Go to Settings in the menus and choose Edit all.

In the new window that appears type “oval" in the search box.

Double click the default value for cartoon_oval_length, enter your chosen 
preference, and hit the enter key on your keyboard.

You should see your change.

2) If this doesn’t work, you see no change, then the selection for your chosen 
object has been directly modified by script. 

You can check this by opening a new PyMOL session and open any pdb file. Apply 
the default changes to cartoon oval length as described above in #1, if it 
works, then #2 needs to be changed.

To change #2, choose the exact same selection that you (or someone else) 
modified in the past and set the cartoon oval length for just that selection… 
set cartoon_oval_length, 0.6, "your selection or pdb name".

On Aug 25, 2014, at 9:57 AM, Hena Dutta  wrote:

> Hi, 
> I am trying to change the cartoon oval length using the command
> set cartoon_oval_length, 0.6
> But, it is not showing any change. I am using pymol 1.6.0.0 in windows 8.1
> Can someone help me?
> Regards,
> Hena
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Re: [PyMOL] Cartoon_oval_length

[H. Adam Steinberg]

Oh thank you, you just made my life so much easier! I always get to work on 
PyMOL sessions after people have tweaked them into oblivion...


On Aug 25, 2014, at 11:40 AM, Thomas Holder  
wrote:

> Hi Hena and Adam,
> 
> the shortcut to solve what Adam is describing in #2 would be:
> 
> PyMOL> unset cartoon_oval_length, *
> 
> That clears the setting on all objects and falls back to using the global 
> setting.
> 
> Cheers,
>  Thomas
> 
> On 25 Aug 2014, at 12:26, H. Adam Steinberg  
> wrote:
>> 1) Go to Settings in the menus and choose Edit all.
>> 
>> In the new window that appears type “oval" in the search box.
>> 
>> Double click the default value for cartoon_oval_length, enter your chosen 
>> preference, and hit the enter key on your keyboard.
>> 
>> You should see your change.
>> 
>> 2) If this doesn’t work, you see no change, then the selection for your 
>> chosen object has been directly modified by script. 
>> 
>> You can check this by opening a new PyMOL session and open any pdb file. 
>> Apply the default changes to cartoon oval length as described above in #1, 
>> if it works, then #2 needs to be changed.
>> 
>> To change #2, choose the exact same selection that you (or someone else) 
>> modified in the past and set the cartoon oval length for just that 
>> selection… set cartoon_oval_length, 0.6, "your selection or pdb name".
>> 
>> On Aug 25, 2014, at 9:57 AM, Hena Dutta  wrote:
>> 
>>> Hi, 
>>> I am trying to change the cartoon oval length using the command
>>> set cartoon_oval_length, 0.6
>>> But, it is not showing any change. I am using pymol 1.6.0.0 in windows 8.1
>>> Can someone help me?
>>> Regards,
>>> Hena
> 
> -- 
> Thomas Holder
> PyMOL Developer
> Schrödinger, Inc.

H. Adam Steinberg
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608/592-2366


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Re: [PyMOL] representing missing residues in pymol

[H. Adam Steinberg]

This is not as simple as you would like but PyMOL does have the ability to 
manually build in missing atoms. And this feature allows you to manually fill 
in missing sequences. I have used it many times to make a specific point, 
noting that the missing AAs were manually added to the figure.

On Sep 25, 2014, at 8:38 AM, ccp4 pymol  wrote:

> Thank you Thomas.
> 
> Best Regards
> Priyan
> 
> On Thu, Sep 25, 2014 at 5:23 PM, Thomas Holder 
>  wrote:
> Hi Priyan,
> 
> unfortunately PyMOL doesn't have such functionality to include missing atoms 
> in the sequence viewer, neither does it read SEQRES records.
> 
> Cheers,
>   Thomas
> 
> On 21 Sep 2014, at 23:28, Priyadarshan  wrote:
> > Hello everyone
> >
> >  Many a times we have structures solved with residues missing as no 
> > electron density was seen. The complete sequence information is given in 
> > the SEQRES section of PDB. Is there a way in which we can identify the 
> > missing residues readily when we turn on the sequence feature by may be 
> > putting it in small letters or italicized etc. This would be like asking 
> > pymol to read sequence from SEQRES section and compare it to sequence from 
> > the section where coordinates are.
> >
> > I am sorry if such a post/request has already been made but I could not 
> > find it. Please suggest/direct.
> >
> > Thank you.
> 
> --
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> PyMOL Developer
> Schrödinger, Inc.
> 
> 
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Re: [PyMOL] rendering missing segments

[H. Adam Steinberg]

Phenomenal idea! I fully agee! :)

On Sep 27, 2014, at 2:22 AM, Seth Harris  wrote:

> Hi Thomas et al,
> 
> There was a recent question on the board about missing residues and the 
> possibility of reading SEQRES headers and PyMOL being able to show the 
> missing bits in the sequence view, perhaps with the amino acid letters grayed 
> out to distinguish the gap. I know the reply was "PyMOL doesn't currently" do 
> this, but it seemed to then end "full stop" rather than, "...but it's a 
> fantastic idea". I'd like to second the idea as a great addition! When 
> building structures or viewing and hitting gaps one always has to shuffle off 
> to find the sequence or jump back to see how big the gap is and what type of 
> residues are supposed to be in there. This would put it right there 
> integrated at one's fingertips.
> 
> This also reminds me of something I suggested to you, Thomas, that might fit 
> in here of having a "cartoon dash" rendering (at least for loops if not 
> helices and strands?) such that one could borrow a loop from a homologue or 
> build in a placeholder to provide visual continuity in a model while still 
> clearly indicating the disordered regions, but now in a 3D ray-traced dashed 
> line that follows the cartoon trajectory rather than the usual penciled in 
> job.
> 
> I know in building a new structure I don't often have any SEQRES header in 
> place, but if it offered advantages like this it would be easy enough to 
> install such.
> 
> Thanks,
> Seth
> 
>  
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Re: [PyMOL] ray trace mode 1 playing up pymol 1.7.4?

[H. Adam Steinberg]

The thickness, or weight of the black outline is related to the size of the 
viewport or the ray command.

If you ray the image larger, the thickness of the black outline will be greatly 
reduced. This will improve the clarity of colored sphere surface by reducing 
the amount of black in those areas.

I would try using surface instead of spheres to make the black outline work in 
a more cleaner style. If you want to stick with spheres, remove the black 
outline and use ambient occlusion lighting:

set light_count,8
set spec_count,1
set shininess, 10
set specular, 0.25
set ambient,0
set direct,0
set reflect,1.5
set ray_shadow_decay_factor, 0.1
set ray_shadow_decay_range, 2
unset depth_cue


> On Dec 15, 2014, at 4:33 AM, Jacob Lewis  wrote:
> 
> Hi, 
> 
> I have a very complicated image to render in pymol and everytime I go to 
> render it in colour with a black outline in spheres I get the render below 
> whereby all the spheres have messing black lines in them? How do I circumvent 
> this? 
> 
> 
> Cheers, 
> 
> Jacob
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Re: [PyMOL] Clip surface only

[H. Adam Steinberg]

if you have access to Gimp or photoshop and want to do this in just a few 
minutes… clip and render the surface how you want it, then without moving 
anything, unclip and render just the ligand. In any bitmap editing program 
layer the ligand image over the clipped surface image and merge the two into 
one image.


> On Jan 21, 2015, at 2:57 PM, Markus Heller  wrote:
> 
> Hello all,
> 
> I'm trying to show a ligand in a binding site, and I'd like to selectively 
> clip the surface only.  I haven't found anything on the web, only that it was 
> not possible a few years ago.
> 
> Surely this has changed?
> 
> Thanks and Cheers
> Markus
> 
> 
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Re: [PyMOL] cartoon_highlight_color for specific regions of structure?

[H. Adam Steinberg]

If you make each chain a separate object, then you can apply a different 
highlight color to each obj.

Select each chain and extract it or copy it to a new obj.

set cartoon_highlight_color, yellow, obj01
set cartoon_highlight_color, red, obj02
set cartoon_highlight_color, blue, obj03
etc.

> On Feb 4, 2015, at 4:22 PM, Thomas Holder  
> wrote:
> 
> Hi Gregg,
> 
> cartoon_highlight_color is currently not implemented on the atom-level, so 
> setting it for an atom selection has no effect.
> 
> The next PyMOL version will print a warning if a setting is set on an 
> unsupported level.
> 
> Cheers,
>  Thomas
> 
> On 01 Feb 2015, at 01:20, Gregg Wells  wrote:
> 
>> Can cartoon_highlight_color be applied to specific regions of a protein 
>> structure?  
>> 
>> For example, I am viewing PDB file 2bg9 in the cartoon mode, with each chain 
>> in a different color.  My PyMOL version is 1.7.4.1 running on a 64-bit 
>> Windows computer.
>> 
>> The command:
>>  set cartoon_highlight_color, yellow
>> does what is expected.  The interiors of all helices of all chains become 
>> yellow.
>> 
>> However, for more specific coloring, I want the helix interiors only of 
>> chain B to display as yellow.
>> When I start with a cartoon display of PDB file 2bg9, the command:
>>  set cartoon_highlight_color, yellow, /Unwin_4Ang_2bg9//B
>> does nothing.  PyMOL seems to accept the command and displays no error 
>> message.
>> 
>> Should cartoon_highlight_color be able to change the interior color of 
>> specific regions of a protein structure?  If Yes, then what is wrong with 
>> the command
>>  set cartoon_highlight_color, yellow, /Unwin_4Ang_2bg9//B
>> 
>> What is the correct syntax for applying cartoon_highlight_color to specific 
>> selections of a protein?
>> 
>> Thanks.
>> 
>> Gregg
> 
> -- 
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> 
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[PyMOL] what color was used?

[H. Adam Steinberg]

I am creating a new PyMOL session and I have to match the colors that someone 
else used in a different PyMOL session. Is there any way to identify what 
colors they used for an obj or sele?


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Re: [PyMOL] what color was used?

[H. Adam Steinberg]

Thank you Matt!

> On Feb 27, 2015, at 4:24 PM, Matthew Baumgartner  wrote:
> 
> Hi Adam,
> You can retrieve them using the iterate method.
>  See: http://pymolwiki.org/index.php/Color#Getting_Atom_Colors 
> <http://pymolwiki.org/index.php/Color#Getting_Atom_Colors>
> 
> HTH,
> Matt Baumgartner
> 
> 
> On 2/27/2015 4:28 PM, H. Adam Steinberg wrote:
>> I am creating a new PyMOL session and I have to match the colors that 
>> someone else used in a different PyMOL session. Is there any way to identify 
>> what colors they used for an obj or sele?
>> 
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366
>> 
>> 
>> 
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Re: [PyMOL] green rings

[H. Adam Steinberg]

I continually have this same issue.

When we change the color of an object, the fill color of the ring should also 
change to that same color. It is very annoying to have it stay default green.

If you change the color of the ring fill to something other than green, then 
close the pse file, and open it at a later date, all of the ring fills colors 
default back to green!

Is there anyway to change the code so the ring fill color changes with the user 
selection, and then not have it revert back to green when we open the file at a 
later date?


> On Mar 9, 2015, at 10:20 AM, Quentin Vicens  wrote:
> 
> Hi folks,
> 
> I'm wondering how to get rid of the default green shine that's present in the 
> middle of every ring (see attached snapshot) following commands such as:
> spectrum count,blue_white_red
> set cartoon_ladder_mode,4
> set cartoon_ring_mode,3
> set cartoon_ring_finder,2
> 
> Thanks in advance for any help!
> Quentin
> 
> Quentin Vicens
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Re: [PyMOL] green rings

[H. Adam Steinberg]

Thank you!

> On Mar 10, 2015, at 9:07 AM, Thomas Holder  
> wrote:
> 
> Hi Quentin, Adam, David, Francis,
> 
> I just looked at the code, color is hardcoded if "ring_color" is default. 
> We'll fix that.
> 
> Francis, I assume you used an rather old PyMOL version, I confirm that I get 
> the expected color with PyMOL 1.2.
> 
> Cheers,
>  Thomas
> 
> On 10 Mar 2015, at 09:56, Quentin Vicens  wrote:
> 
>> Thanks Francis - I tried just that and it's green with version 1.7.2.1!!
>> Quentin
>> 
>> On 10 Mar 2015, at 14:51, Francis Reyes  wrote:
>> 
>>> Strange,
>>> 
>>> I load 2GIS.pdb
>>> 
>>> show cartoon
>>> hide lines
>>> set cartoon_ring_mode, 3
>>> spectrum count, blue_white_red
>>> 
>>> and I get 
>>> 
>>> 
>>> No green in the rings? 
>>> 
>>> PyMOL 1.4.
>>> 
>>> 
>>> F
>>> On Mar 9, 2015, at 11:20 AM, Quentin Vicens  wrote:
>>> 
>>>> Hi folks,
>>>> 
>>>> I'm wondering how to get rid of the default green shine that's present in 
>>>> the middle of every ring (see attached snapshot) following commands such 
>>>> as:
>>>> spectrum count,blue_white_red
>>>> set cartoon_ladder_mode,4
>>>> set cartoon_ring_mode,3
>>>> set cartoon_ring_finder,2
>>>> 
>>>> Thanks in advance for any help!
>>>> Quentin
>>>> 
>>>> Quentin Vicens
>>>> Tél : +33 (0)3 88 41 70 42
>>>> Tél 2 : +33 (0)7 61 37 83 10
>>>> Fax : +33 (0)3 88 60 22 18
>>>> qvic...@unistra.fr
>>>> 
>>>> UPR9002-CNRS-University of Strasbourg
>>>> Institut de Biologie Moléculaire et Cellulaire
>>>> 15 rue René Descartes
>>>> F - 67084 Strasbourg 
>>>> http://www-ibmc.u-strasbg.fr/arn/Eriani/equi_Eriani_fr.php
>>>> 
>>>> 
>>>> 
> 
> 
> -- 
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> 
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Re: [PyMOL] pymol crash when ray

[H. Adam Steinberg]

one more thing…

Delete all objects that you are not using for this particular rendering (save 
it as a separate file). I have found this speeds up rendering times.


> On Apr 14, 2015, at 7:49 PM, H. Adam Steinberg  
> wrote:
> 
> For an instantaneous rendering of any PyMOL scene that won't crash your 
> machine use the DRAW command instead of the RAY command. You will loose 
> features like shadows and depth cue.
> 
> When I have to render huge PyMOL scenes like you describe below, I create 
> them in a way that I can RAY them in sections (for example, ray the back 
> section, then the front) and then reassemble those sections in Photoshop.
> 
> You can also change how PyMOL uses memory from the Settings menu. Choose 
> Settings/Rendering/Memory and then choose use most, but I seem to remember 
> there is some limitation that actually makes PyMOL render without crashing 
> when you choose use less.
> 
>> On Apr 14, 2015, at 3:12 PM, m...@mskcc.org <mailto:m...@mskcc.org> wrote:
>> 
>> Hi pymol users,
>> 
>> I am just using pymol to open one super big molecular model (20 
>> megadaltons). My pymol1.7 is on linux system and the computer has 32 CPU 
>> with 62GB memory storage.
>> When I try to use command ray to make a high quality image, the pymol crash 
>> with error message like this: Pymol ran out of memory storage and you need 
>> to decease the quality of the image. 
>> 
>> I have tried to set the hash_max 10, 30 or 60 and it won’t work. Also I use 
>> protein backbone to present the whole structure.
>> I will appreciate any suggestions.
>> 
>> Thanks,
>> Wenfu
>> 
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> 

H. Adam Steinberg
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608/592-2366

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Re: [PyMOL] Beginning with PyMol

[H. Adam Steinberg]

I’ve always wonder why this isn’t available on the Mac version.


> On Apr 19, 2015, at 8:58 AM, Thomas Holder  
> wrote:
> 
> Hi Rajib & Yuktimmana,
> 
> you can interactively build molecules using the builder:
> http://pymolwiki.org/index.php/Builder
> 
> Enjoy!
> 
> Cheers,
>  Thomas
> 
> On 19 Apr 2015, at 08:03, bkpsusmitaa  wrote:
>> Dear Sir / Madam,
>> My daughter and I are novices in PyMol. We have only just begun! :) I
>> have seen the page
>> http://www.pymolwiki.org/index.php/Practical_Pymol_for_Beginners.
>> Begins with a protein molecule.
>> We use the PyMol package from the Debian Repository in a Knoppix system.
>> How can we begin by building a simple molecule, say, methane, or
>> carbon tetrachloride, or butylene?
>> Eagerly awaiting your reply,
>> Rajib & Yuktimmana
> 
> -- 
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> --
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> Develop your own process in accordance with the BPMN 2 standard
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[PyMOL] Cryo-EM structures

[H. Adam Steinberg]

Hi All,

I’m looking for a primer on how to manipulate and render Cryo-EM structures in 
PyMOL. Does anyone have any suggestions where I can start?

As a test I downloaded a structure and applied a map to it, but I was only able 
to give it one color. How do you get multiple colors, like this example? 
<http://sourceforge.net/p/pymol/screenshot/Screen%20Shot%202012-12-14%20at%2010.51.28%20AM.png
 
<http://sourceforge.net/p/pymol/screenshot/Screen%20Shot%202012-12-14%20at%2010.51.28%20AM.png>>

And what are the common databases where I can find Cryo-EM structures?
<http://www.ebi.ac.uk/pdbe/ <http://www.ebi.ac.uk/pdbe/>>
<http://pdbj.org/emnavi/ <http://pdbj.org/emnavi/>>

Thank you for any help you can provide.


H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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[PyMOL] bonding nucleic acid bases

[H. Adam Steinberg]

Hi all,

If I create a string of double-strand DNA, or take a string of double-strand 
DNA or RNA from a structure, is there any automated way to have the bases link 
AT, UA, GC, so when I manually sculpt or deform the DNA those bases would stay 
together?

I could go through the structure and manually create physical bonds where the 
hydrogen bonds would be, and that would work, but I’m wondering if anyone has a 
script or is there a function that I am unaware of?

Thanks!

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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[PyMOL] bonding nucleic acid bases

[H. Adam Steinberg]

Hi all,

If I create a string of double-strand DNA, or take a string of double-strand 
DNA or RNA from a structure, is there any automated way to have the bases link, 
AT, UA, GC, so when I manually sculpt or deform the DNA those bases would stay 
together?

I could go through the structure and manually create physical bonds where the 
hydrogen bonds would be, and I’m guessing that would work, but I’m wondering if 
anyone has a script or is there a function that I am unaware of?

Thanks!

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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[PyMOL] working with ccp4 maps

[H. Adam Steinberg]

I have some questions about working with cryo-tomography maps in PyMOL.
Once you create an isosurface from a map, how do you move it?
How do you color part of a map?

I am trying to recreate the attached image using different colors and a 
different orientation.

The maps are EMDB-2329 (central hub) and EMDB-2330 (one triplet that I have to 
show nine times).



H. Adam Steinberg
7904 Bowman Rd
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608/592-2366

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[PyMOL] test message

[H. Adam Steinberg]

Hi Thomas,

I’ve sent a few messages to the pymol users list over the last few weeks, the 
messages show up on the web site for the list, but they don’t come to my email 
inbox like the other messages that people send to the list do. Also no one has 
replies to any of them so I’m thinking I have a setting set wrong. Do you have 
any idea if there is a setting I have messed up with the listserv? Or if I’ve 
been blacklisted for some reason?

Thanks,

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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Re: [PyMOL] test message

[H. Adam Steinberg]

Thanks Thomas.

> On Jul 2, 2015, at 2:46 PM, Thomas Holder  
> wrote:
> 
> Hi Adam,
> 
> Your messages have been delivered to the list, everything's all right. The 
> default setup is that you don't receive duplicates of your own messages (I 
> can change that for you if you want).
> 
> I assume nobody replied to your message "bonding nucleic acid bases" simply 
> because nobody had written such a script before (I think that's what you were 
> asking for).
> 
> Cheers,
>  Thomas
> 
> On 02 Jul 2015, at 15:36, H. Adam Steinberg  
> wrote:
> 
>> Hi Thomas,
>> 
>> I’ve sent a few messages to the pymol users list over the last few weeks, 
>> the messages show up on the web site for the list, but they don’t come to my 
>> email inbox like the other messages that people send to the list do. Also no 
>> one has replies to any of them so I’m thinking I have a setting set wrong. 
>> Do you have any idea if there is a setting I have messed up with the 
>> listserv? Or if I’ve been blacklisted for some reason?
>> 
>> Thanks,
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366
> 
> -- 
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


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Re: [PyMOL] bonding nucleic acid bases

[H. Adam Steinberg]

Thank you! I can't wait to try it!

> On Jul 2, 2015, at 3:05 PM, Thomas Holder  
> wrote:
> 
> Hi Adam,
> 
> The attached script will create covalent bonds for all polar contacts between 
> two selections.
> 
> Example:
> run 
> https://github.com/Pymol-Scripts/Pymol-script-repo/raw/master/get_raw_distances.py
> run bond_hbonds.py
> fetch 1nz1, async=0
> bond_hbonds resi 1-12, resi 12-22 
> 
> Hope that helps.
> 
> Cheers,
>  Thomas
> 
> 
> On 23 Jun 2015, at 22:51, H. Adam Steinberg  
> wrote:
> 
>> Hi all,
>> 
>> If I create a string of double-strand DNA, or take a string of double-strand 
>> DNA or RNA from a structure, is there any automated way to have the bases 
>> link, AT, UA, GC, so when I manually sculpt or deform the DNA those bases 
>> would stay together?
>> 
>> I could go through the structure and manually create physical bonds where 
>> the hydrogen bonds would be, and I’m guessing that would work, but I’m 
>> wondering if anyone has a script or is there a function that I am unaware of?
>> 
>> Thanks!
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366
> 
> -- 
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


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[PyMOL] secondary structure disappears

[H. Adam Steinberg]

Hi All,If you fetch 3ow9 in PyMOL,split_states to get all six of the strands,select all, then copy to object,You only get the two strands, not all six, I need all six to be duplicated into one object so I can make a long amyloid fibril.If I open the pdb file for 3ow9 in text edit and remove all the text for the individual models (and the waters), then open that file in PyMOL I get all six strands, but all the cartoon secondary structure is missing except for the two original strands. I tired running the alter command in PyMOL, it changes the secondary structure in the other objects I have open but not in this pdb.I see the Sheet entry in the pdb file but I don’t know how to duplicate and change the sheet entry so it applies to the other four strands in the file.Could someone point me to a place on the web that explains how to change the sheet entry (I’d like to learn how to do it)? or tell me how to fix this pdb file?Thanks!

3ow9.pdb
Description: Protein Databank data

H. Adam Steinberg7904 Bowman RdLodi, WI 53555608/592-2366


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Re: [PyMOL] secondary structure disappears

[H. Adam Steinberg]

The secondary structure is only there for the first set of strands, and then 
that is used for the other strands when you split_states, but how do I change 
that entry so it applies to the other strands?

Here is that entry from the file that I attached:

SHEET1   A 2 LEU A   2  PHE A   5  0
SHEET2   A 2 LEU B   2  PHE B   5 -1  O  VAL B   3   N  PHE A   4  

> On Jul 23, 2015, at 10:48 AM, Smith Liu  wrote:
> 
> I think the secondary structure record (SS) has been lost during your 
> splitting. So just add and edit the SS record in the PDB file to the lost 
> ones.
> 
> Smith
> 
> 
> 
> 
> 
> At 2015-07-23 22:23:24, "H. Adam Steinberg"  
> wrote:
> Hi All,
> 
> If you fetch 3ow9 in PyMOL,
> split_states to get all six of the strands,
> select all, then copy to object,
> You only get the two strands, not all six, I need all six to be duplicated 
> into one object so I can make a long amyloid fibril.
> 
> If I open the pdb file for 3ow9 in text edit and remove all the text for the 
> individual models (and the waters), then open that file in PyMOL I get all 
> six strands, but all the cartoon secondary structure is missing except for 
> the two original strands. I tired running the alter command in PyMOL, it 
> changes the secondary structure in the other objects I have open but not in 
> this pdb.
> 
> I see the Sheet entry in the pdb file but I don’t know how to duplicate and 
> change the sheet entry so it applies to the other four strands in the file.
> 
> Could someone point me to a place on the web that explains how to change the 
> sheet entry (I’d like to learn how to do it)? or tell me how to fix this pdb 
> file?
> 
> Thanks!
> 
> 
> 

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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Re: [PyMOL] secondary structure disappears

[H. Adam Steinberg]

Big thank you to all of you!

I really need to find some time to better learn code. :/


> On Jul 23, 2015, at 4:36 PM, Sampson, Jared  wrote:
> 
> I'm posting the following solution on behalf of Thomas Holder (whose 
> sourceforge.net <http://sourceforge.net/> email address is currently down due 
> to SF server issues), to ensure it is added to this thread in the archive:
> 
>> This is due to chain identifier conflict. He's merging 6 models with 
>> identical identifiers. A simple fix would be:
>> 
>> fetch 3ow9, type=pdb1, async=0
>> split_states 3ow9
>> alter 3ow9_000*, segi=model[-1]
>> create combined, 3ow9_000*
> 
> Changing the chain IDs as Rob suggested would also work.
> 
> Cheers,
> 
> Jared
> 
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/ <http://kong.med.nyu.edu/>
> 
> 
> 
> 
> 
> 
> On Jul 23, 2015, at 2:42 PM, Robert Campbell  <mailto:robert.campb...@queensu.ca>> wrote:
> 
>> Hi Adam,
>> 
>> I think you also want to make sure that each strand as a distinct chain
>> ID if you want the cartoon representation to work correctly.
>> 
>> Unfortunately that means you have to use "alter" but to change the
>> chain IDs on the objects created by the split_states command before
>> merging them all into one object.
>> 
>> It worked for me when I tried that with 3ow9.
>> 
>> Cheers,
>> Rob
>> 
>> On Thu, 2015-07-23 09:23 EDT, "H. Adam Steinberg"
>> mailto:h.adam.steinb...@gmail.com>> wrote:
>> 
>>> Hi All,
>>> 
>>> If you fetch 3ow9 in PyMOL,
>>> split_states to get all six of the strands,
>>> select all, then copy to object,
>>> You only get the two strands, not all six, I need all six to be
>>> duplicated into one object so I can make a long amyloid fibril.
>>> 
>>> If I open the pdb file for 3ow9 in text edit and remove all the text
>>> for the individual models (and the waters), then open that file in
>>> PyMOL I get all six strands, but all the cartoon secondary structure
>>> is missing except for the two original strands. I tired running the
>>> alter command in PyMOL, it changes the secondary structure in the
>>> other objects I have open but not in this pdb.
>>> 
>>> I see the Sheet entry in the pdb file but I don’t know how to
>>> duplicate and change the sheet entry so it applies to the other four
>>> strands in the file.
>>> 
>>> Could someone point me to a place on the web that explains how to
>>> change the sheet entry (I’d like to learn how to do it)? or tell me
>>> how to fix this pdb file?
>>> 
>>> Thanks!
>>> 
>>> 
>>> 
>>> H. Adam Steinberg
>>> 7904 Bowman Rd
>>> Lodi, WI 53555
>>> 608/592-2366
>>> 
>> 
>> 
>> 
>> 
>> -- 
>> Robert L. Campbell, Ph.D.
>> Senior Research Associate/Adjunct Assistant Professor
>> Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
>> Queen's University, 
>> Kingston, ON K7L 3N6  Canada
>> Tel: 613-533-6821
>> mailto:robert.campb...@queensu.ca>>  
>> http://pldserver1.biochem.queensu.ca/~rlc 
>> <http://pldserver1.biochem.queensu.ca/~rlc>
>> 
>> --
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[PyMOL] change electrostatic ramp color?

[H. Adam Steinberg]

I opened a complex .pse file I created back in 2007 and the electrostatic ramp 
is showing as green to blue. Any ideas how to change it back to red to blue?

The wiki seems to be down.

H. Adam Steinberg
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Re: [PyMOL] lipid membrane help

[H. Adam Steinberg]

You could also do this in sections building up to the amount of lipids you need.
Create and Rotate 3 lipids.
Select, Duplicate and rotate one set of three so you now have 6 lipids.
Select, Duplicate and rotate on set of 6 so you now have 12 lipids.
Continue on…+



> On Oct 19, 2015, at 9:23 AM, Osvaldo Martin  wrote:
> 
> Hi Nhi,
> 
> You can use the Rotate <http://pymolwiki.org/index.php/Rotate>. You just need 
> to specify the correct selection. If you have any other doubt, please ask.
> 
> Cheers,
> Osvaldo.
> 
> On Mon, Oct 12, 2015 at 9:45 PM, Tran,Nhi T  <mailto:nhittra...@gmail.com>> wrote:
> 
> 
> 
> I want to rotate the lipid molecules in the outer leaflet to form a concave 
> surface. How do I do this without having to rotate each lipid individually?
> 
> Any suggestions would be greatly appreciated!
> 
> Best,
> Nhi
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Re: [PyMOL] change electrostatic ramp color?

[H. Adam Steinberg]

Thank you Osvaldo for taking time to answer all the questions this morning!

I tried but failed to recolor the ramp. 

Then an idea hit me, maybe the red in the ramp was changed to green so I opened 
the color setting panel and yes, the red was changed to green. I don’t remember 
why since that file was created 8 years back…

So I changed it back to a “real” red and generated a new map - all is back! 

Thanks!


> On Oct 19, 2015, at 9:14 AM, Osvaldo Martin  wrote:
> 
> Hi Adam,
> 
> Now that the PyMOL wiki is back, did you find the solution at the Ramp_New <> 
> Wiki page?
> 
> Cheers,
> 
> Osvaldo.
> 
> On Fri, Oct 16, 2015 at 9:10 PM, H. Adam Steinberg 
> mailto:h.adam.steinb...@gmail.com>> wrote:
> 
> 
> 
> I opened a complex .pse file I created back in 2007 and the electrostatic 
> ramp is showing as green to blue. Any ideas how to change it back to red to 
> blue?
> 
> The wiki seems to be down.
> 
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366 
> 
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Re: [PyMOL] PyMOLWiki: Quick Update

[H. Adam Steinberg]

Thank you Jason!

> On Oct 19, 2015, at 9:34 PM, Jason Vertrees  wrote:
> 
> Greetings Shane, et. al.,
> 
> The issue with the database connection should be fixed permanently now. 
> Search should also be consistently better.
> 
> I've independently owned and run the wiki for almost a decade now. It's 
> heading toward 22 million page views. Anyhow, it's now on good hardware (SSD, 
> lots of RAM, and a nice network) and should be stable. Let me know if not.
> 
> Cheers,
> 
> -- Jason
> 
> On Sun, Oct 18, 2015 at 6:35 PM Shane Caldwell  <mailto:shane.caldwel...@gmail.com>> wrote:
> Hi Jason, pymol-users list,
> 
> The pymolwiki seems to be down and has been for a few days now. It looks like 
> the server's down?
> 
> Any page returns:
> 
> (Can't contact the database server: Can't connect to local MySQL server 
> through socket '/var/run/mysqld/mysqld.sock' (111) (localhost))
> 
> Is there a mirror anywhere that can be used?
> 
> Shane Caldwell
> McGill University
> 
> On Wed, Sep 9, 2015 at 1:02 AM, Jason Vertrees  <mailto:jason.vertr...@gmail.com>> wrote:
> Greetings,
> 
> It's been a while, I hope this message finds everyone well. 
> 
> I'm writing to briefly let you know that I recently moved, upgraded, and 
> reinstalled/fixed search on the PyMOLWiki. It should be, hopefully, fast and 
> more useful. Feel free to report any bugs.
> 
> Back to the startup-life.
> 
> Cheers,
> 
> -- Jason
> 
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Re: [PyMOL] real time minization in Pymol

[H. Adam Steinberg]

I would love to see this feature improved!

Try it out if you have never used it. It works quite well. It is quite 
processor intensive and it can take over your computer when it is running…. I 
have also found when you uncheck it in the menu, it will still continue to run 
and I end up force quitting to get it to stop.

> On Nov 23, 2015, at 8:46 AM, Albert  wrote:
> 
> Hello:
> 
> I just found a a very nice module of pymol, called "Molecular 
> Sculpting". However, according to the description in Pymolwiki, it works 
> like a real-time energy minimizer, except that it isn't minimizing the 
> energy. Instead, its just trying to return local atomic geometries 
> (bonds, angles, chirality, planarity) to the configuration the molecules 
> possess when they were first loaded into PyMOL.
> 
> So I am just wondering does the developer have any planning to improve 
> this nice too? For instance introducing forcefiled for this tool (eg: 
> Amber FF for protein, GAFF for the ligand). There is a "optimize" plugin 
> in Pymol, maybe the developer can consider merge them together?
> 
> Thank you very much
> 
> Albert
> 
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[PyMOL] Brownian motion in movie?

[H. Adam Steinberg]

<https://www.youtube.com/watch?v=aNl7z0MOAVM 
<https://www.youtube.com/watch?v=aNl7z0MOAVM>>

Does anyone know how CompChemist made the Brownian motion in the movie? I would 
really like to duplicate that effect!

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[PyMOL] JyMOL vs JSMol

[H. Adam Steinberg]

I looked up JyMOL and found the basic definition but need more details. Can 
someone give me a link or provide the info?

Currently using JSMol but that is limited in what it can do and I cannot use 
any of my PyMOL files in JSMol. 

My Main question is, could I use JyMOL to replace JSMol? Or is JyMOL more 
equivalent to JMol?

Thanks!

H. Adam Steinberg
7904 Bowman Rd
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Re: [PyMOL] JyMOL vs JSMol

[H. Adam Steinberg]

Wow!!! do I need to apologize for for stating "that I could not use all my 
PyMOL files in Jmol!" I just threw some very complicated .PSE files at Jmol and 
it opened them all competently (so far)! I am very impressed and elated that I 
will not have to rebuild all of these files form scratch.

And yes Bob, if I find something that will not open in Jmol, or something that 
is misrepresented, I will let you know so we can possibly find a way to make it 
work.

Thank you for all your hard work on Jmol and JSmol!


> On Dec 15, 2015, at 6:03 AM, Robert Hanson  wrote:
> 
> I guess I should chime in here. JSmol does read (some fraction of) PyMOL 
> session files. To be sure it has not been a priority to keep up to date with 
> all the amazing PyMOL capabilities, but certainly as a proof of concept it 
> has worked well, and it would be great to collaborate on this to improve it 
> more. See, for example:  http://noys3.weizmann.ac.il/a2jb/browse 
> <http://noys3.weizmann.ac.il/a2jb/browse>
> 
> I certainly don't claim to know anything about JyMOL, except I guess it uses 
> JNLP. Does Chrome support JNLP anymore?
> 
> Bob Hanson
> 

H. Adam Steinberg
7904 Bowman Rd
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608/592-2366

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Re: [PyMOL] [BUG?] Selection by secondary structure - Pymol 1.8.0.0 r4144

[H. Adam Steinberg]

I had this same issue when I was working on Christmas… sorry I forgot to post 
it to the list. I ended up going back to a 1.7.6 version to get it done.

1.8 now distinguishing between upper and lowercase letters This means that the 
old “ss s” is now “ss S”. It’s a bit of a pain for long time users to get used 
to but it will be better for everyone in the long term.

I had to go back and change all my scripts. And that’s fine for me but I worry 
about all the scripts in the wiki… unsuspecting users will try and use one of 
those wiki scripts and have failure. Did all of those scripts get updated?

> On Jan 6, 2016, at 2:49 AM, TUBIANA Thibault CNRS  
> wrote:
> 
> Hello everyone!
> 
> Since the last open source version of pymol (1.8.0.0 r4144) on Python 2.7,
> I'm not able to perform a selection by secondary structure except with coil
> example : 
> color red, ss s #not working (no error message)
> color red, ss h #not working (no error message)
> color red, ss s #works
> Did the selector change since the last version or is that a bug ?
> 
> Happy 2016 to all,
> Regards,
> Thibault Tubiana.
> 
> --
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Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

[H. Adam Steinberg]

Tsjerk,

Can you add an example of generating a “real” membrane around a protein to the 
gallery of the PyMOLwiki?

My students would love to have easy access to that!

Thanks!

Adam

> On Feb 2, 2016, at 1:39 AM, Tsjerk Wassenaar  wrote:
> 
> Hi Annemarie,
> 
> It's actually quite simple to generate a real membrane around your protein 
> and, e.g., to show the head groups. Do you have a PDB ID for the protein, or 
> are they in-house models?
> 
> Cheers,
> 
> Tsjerk
> 
> On Mon, Feb 1, 2016 at 10:57 PM, Julian Heinrich  <mailto:jul...@joules.de>> wrote:
> Hi Annemarie,
> 
> Have you tried the following?
> cmd.translate([x,y,z], object='membrane')
> 
> replace x,y,z with your translation vector.
> 
> Cheers,
> Julian
> 
> On Sat, Jan 30, 2016 at 8:33 AM, Honegger Annemarie  <mailto:honeg...@bioc.uzh.ch>> wrote:
> I am trying to show some cell surface receptors and to indicate their 
> position relative to the membrane.
> 
> I thought to indicate the plane of the membrane by a flat disk, a ago 
> cylinder.
> 
> x1,y1,z1 = 0, -1, 0 # start point
> r1,g1,b1 = 1, 1, 0 # color (yellow)
> x2,y2,z2 = 0, -2, 0 # end point
> r2,g2,b2 = 1, 1, 0 # color (yellow)
> radius = 100
> cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, b2 
> ], "membrane" )
> 
> When I try to move this cylinder into the correct position with 
> cmd.transform_selection,
> using the transformation parameters extracted from get_view (reordering them 
> as needed)
> I get the error message "Selector-Error: Invalid selection name “membrane” “
> 
> The same transform command works fine if I apply it to a pseudo atom 
> originally generated with coordinates 0,0,0.
> 
> Any suggestion how else I could indicate the membrane, or how I could place 
> my ego object parallel 
> to the screen yz plane? I have to be able to do this in a reproducible 
> fashion, as I have to  do this
> for a large number of constructs that bend my receptors relative to the 
> membrane in various ways. 
> 
> Thanks for your help
>   Annemarie
>   
> ___
> 
> Dr. Annemarie Honegger PhD
> Department 
> of Biochemistry
> Zürich University
> Winterthurerstrasse 190
> CH-8057 Zürich
> Switzerland
> 
> 
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Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

[H. Adam Steinberg]

Thank you Tsjerk. What we do right now is just open VMD and use the membrane 
builder, then take that file back into PyMOL!

> On Feb 3, 2016, at 12:29 PM, Tsjerk Wassenaar  wrote:
> 
> Hi Adam,
> 
> Well, for putting it on the Pymol wiki, I'll at least have to wait and see 
> how far my students got with integrating the routine in a webservice. If they 
> already managed, it will be as easy as submitting the structure and saying 
> what membrane you want. Otherwise, it will require some downloads and 
> installs to get the proper programs in place, before it becomes as simple as 
> running a single command specifying the protein and membrane.
> 
> If you and your students would like to try it out, I can give some pointers 
> and provide my scripts to get it done. The wiki will have to wait a bit, but 
> it will come.
> 
> Cheers,
> 
> Tsjerk
> 
> On Feb 2, 2016 5:33 PM, "H. Adam Steinberg"  <mailto:h.adam.steinb...@gmail.com>> wrote:
> Tsjerk,
> 
> Can you add an example of generating a “real” membrane around a protein to 
> the gallery of the PyMOLwiki?
> 
> My students would love to have easy access to that!
> 
> Thanks!
> 
> Adam
> 
>> On Feb 2, 2016, at 1:39 AM, Tsjerk Wassenaar > <mailto:tsje...@gmail.com>> wrote:
>> 
>> Hi Annemarie,
>> 
>> It's actually quite simple to generate a real membrane around your protein 
>> and, e.g., to show the head groups. Do you have a PDB ID for the protein, or 
>> are they in-house models?
>> 
>> Cheers,
>> 
>> Tsjerk
>> 
>> On Mon, Feb 1, 2016 at 10:57 PM, Julian Heinrich > <mailto:jul...@joules.de>> wrote:
>> Hi Annemarie,
>> 
>> Have you tried the following?
>> cmd.translate([x,y,z], object='membrane')
>> 
>> replace x,y,z with your translation vector.
>> 
>> Cheers,
>> Julian
>> 
>> On Sat, Jan 30, 2016 at 8:33 AM, Honegger Annemarie > <mailto:honeg...@bioc.uzh.ch>> wrote:
>> I am trying to show some cell surface receptors and to indicate their 
>> position relative to the membrane.
>> 
>> I thought to indicate the plane of the membrane by a flat disk, a ago 
>> cylinder.
>> 
>> x1,y1,z1 = 0, -1, 0 # start point
>> r1,g1,b1 = 1, 1, 0 # color (yellow)
>> x2,y2,z2 = 0, -2, 0 # end point
>> r2,g2,b2 = 1, 1, 0 # color (yellow)
>> radius = 100
>> cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, b2 
>> ], "membrane" )
>> 
>> When I try to move this cylinder into the correct position with 
>> cmd.transform_selection,
>> using the transformation parameters extracted from get_view (reordering them 
>> as needed)
>> I get the error message "Selector-Error: Invalid selection name “membrane” “
>> 
>> The same transform command works fine if I apply it to a pseudo atom 
>> originally generated with coordinates 0,0,0.
>> 
>> Any suggestion how else I could indicate the membrane, or how I could place 
>> my ego object parallel 
>> to the screen yz plane? I have to be able to do this in a reproducible 
>> fashion, as I have to  do this
>> for a large number of constructs that bend my receptors relative to the 
>> membrane in various ways. 
>> 
>> Thanks for your help
>>  Annemarie
>>  
>> ___
>> 
>> Dr. Annemarie Honegger PhD
>> Department 
>> of Biochemistry
>> Zürich University
>> Winterthurerstrasse 190
>> CH-8057 Zürich
>> Switzerland
>> 
>> 
>> --
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
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>> <mailto:PyMOL-users@lists.sourceforge.net>)
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Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

[H. Adam Steinberg]

WOW! what a great resource! I downloaded an example and played with it in 
PyMOL. They removed the Chains, making selections a little harder, but still a 
great resource!

> On Feb 4, 2016, at 5:26 AM, vincent Chaptal  wrote:
> 
> Hi all, 
> 
> about proteins inserted into membranes, the group of Mark Sansom just 
> published a paper where they describe insertion of the whole 
> membrane-proteins PDB into a bilayer followed by coarse-grain MD and all atom 
> MD, and make the results available to everyone. It would be great if they 
> could make it into a server where we submit our pdb.   
> 
> http://sbcb.bioch.ox.ac.uk/memprotmd/beta/ 
> <http://sbcb.bioch.ox.ac.uk/memprotmd/beta/>
> 
> Stansfeld, P. J., et al. (2015). "MemProtMD: Automated Insertion of Membrane 
> Protein Structures into Explicit Lipid Membranes." Structure.
> 
> 
> vincent
> 
> 
> On 03/02/2016 19:33, H. Adam Steinberg wrote:
>> Thank you Tsjerk. What we do right now is just open VMD and use the membrane 
>> builder, then take that file back into PyMOL!
>> 
>>> On Feb 3, 2016, at 12:29 PM, Tsjerk Wassenaar >> <mailto:tsje...@gmail.com>> wrote:
>>> 
>>> Hi Adam,
>>> 
>>> Well, for putting it on the Pymol wiki, I'll at least have to wait and see 
>>> how far my students got with integrating the routine in a webservice. If 
>>> they already managed, it will be as easy as submitting the structure and 
>>> saying what membrane you want. Otherwise, it will require some downloads 
>>> and installs to get the proper programs in place, before it becomes as 
>>> simple as running a single command specifying the protein and membrane.
>>> 
>>> If you and your students would like to try it out, I can give some pointers 
>>> and provide my scripts to get it done. The wiki will have to wait a bit, 
>>> but it will come.
>>> 
>>> Cheers,
>>> 
>>> Tsjerk
>>> 
>>> On Feb 2, 2016 5:33 PM, "H. Adam Steinberg" >> <mailto:h.adam.steinb...@gmail.com>> wrote:
>>> Tsjerk,
>>> 
>>> Can you add an example of generating a “real” membrane around a protein to 
>>> the gallery of the PyMOLwiki?
>>> 
>>> My students would love to have easy access to that!
>>> 
>>> Thanks!
>>> 
>>> Adam
>>> 
>>>> On Feb 2, 2016, at 1:39 AM, Tsjerk Wassenaar < 
>>>> <mailto:tsje...@gmail.com>tsje...@gmail.com <mailto:tsje...@gmail.com>> 
>>>> wrote:
>>>> 
>>>> Hi Annemarie,
>>>> 
>>>> It's actually quite simple to generate a real membrane around your protein 
>>>> and, e.g., to show the head groups. Do you have a PDB ID for the protein, 
>>>> or are they in-house models?
>>>> 
>>>> Cheers,
>>>> 
>>>> Tsjerk
>>>> 
>>>> On Mon, Feb 1, 2016 at 10:57 PM, Julian Heinrich < 
>>>> <mailto:jul...@joules.de>jul...@joules.de <mailto:jul...@joules.de>> wrote:
>>>> Hi Annemarie,
>>>> 
>>>> Have you tried the following?
>>>> cmd.translate([x,y,z], object='membrane')
>>>> 
>>>> replace x,y,z with your translation vector.
>>>> 
>>>> Cheers,
>>>> Julian
>>>> 
>>>> On Sat, Jan 30, 2016 at 8:33 AM, Honegger Annemarie < 
>>>> <mailto:honeg...@bioc.uzh.ch>honeg...@bioc.uzh.ch 
>>>> <mailto:honeg...@bioc.uzh.ch>> wrote:
>>>> I am trying to show some cell surface receptors and to indicate their 
>>>> position relative to the membrane.
>>>> 
>>>> I thought to indicate the plane of the membrane by a flat disk, a ago 
>>>> cylinder.
>>>> 
>>>> x1,y1,z1 = 0, -1, 0 # start point
>>>> r1,g1,b1 = 1, 1, 0 # color (yellow)
>>>> x2,y2,z2 = 0, -2, 0 # end point
>>>> r2,g2,b2 = 1, 1, 0 # color (yellow)
>>>> radius = 100
>>>> cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, 
>>>> b2 ], "membrane" )
>>>> 
>>>> When I try to move this cylinder into the correct position with 
>>>> cmd.transform_selection,
>>>> using the transformation parameters extracted from get_view (reordering 
>>>> them as needed)
>>>> I get the error message "Selector-Error: Invalid selection name “membrane” 
>>>> “
>>>> 
>>>&

Re: [PyMOL] auto_show_cartoon or similar

[H. Adam Steinberg]

Every year I teach students PyMOL, and the look on their faces when they first 
open a pdb in PyMOL and get a cluster of green sticks… yikes!

YES!!! to the default being secondary structure, ligands as sticks, and metal 
ions as spheres! Add - nucleic acids as cartoon. 

> On Feb 8, 2016, at 10:57 AM, Kumar, Abhinav  wrote:
> 
> Showing metal ions  (and FES clusters etc) as spheres would also be useful.
> 
> Thanks,
> Abhinav
> 
> Abhinav Kumar, PhD
> Senior Scientist, Bioinformatics
> Intrexon, Inc.
> 329 Oyster Point Blvd., South San Francisco, CA 94080
> (650) 597-4072 | aku...@intrexon.com
> 
> 
> 
> From: Thomas Holder [thomas.hol...@schrodinger.com]
> Sent: Monday, February 08, 2016 8:51 AM
> To: Ivan Vulovic; Schubert, Carsten [JRDUS]
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] auto_show_cartoon or similar
> 
> Hi Ivan and Carsten,
> 
> I can take "auto_show_cartoon" as a feature request. It's trivial to 
> implement.
> 
> What also would be nice: automatically showing sticks for ligands. e.g. 
> corresponding to the "not polymer" or the "organic" selection. Thoughts?
> 
> Cheers,
>  Thomas
> 
> On 08 Feb 2016, at 09:07, Schubert, Carsten [JRDUS]  
> wrote:
> 
>> Hi Ivan,
>> 
>> you could either try to overload the “load” function in Pymol (not sure this 
>> is supported) or write your own custom load function under a different name, 
>> which loads the protein, assigns the name of the object, hides lines and 
>> shows the cartoon.
>> 
>> Sorry, this is a rather generic answer but should point you in the right 
>> direction.
>> 
>> Cheers,
>> 
>>Carsten
>> 
>> From: Ivan Vulovic [mailto:i...@uw.edu]
>> Sent: Saturday, February 06, 2016 8:18 PM
>> To: pymol-users@lists.sourceforge.net
>> Subject: [PyMOL] auto_show_cartoon or similar
>> 
>> Hello
>> 
>> Is there a way to make cartoon the default representation, something akin to 
>> "auto_show_lines", but for cartoon? There was some dicussion of this in 2010 
>> (link below) but I haven't found anything more recent that does what I'd 
>> like.
>> 
>> http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734.html
>> 
>> Thanks
>> Ivan
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> 
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Re: [PyMOL] how can we make this kind of figure?

[H. Adam Steinberg]

what’s the reference to the paper?


> On Feb 12, 2016, at 1:39 AM, Albert  wrote:
> 
> 
> 
> Hello
> 
> I found a very nice figure in an article but the author didn't mention
> which software he used for render. I am just wondering is it possible to
> render in the same way in Pymol? I've attached this figure.
> 
> thx a lot
> 
> Albert
> 
> 
> 
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Re: [PyMOL] visualizing a transparent surface within a transparent surface

[H. Adam Steinberg]

I get around this by rendering both items separately and then combining the two 
images in photoshop.

Is there a way to do what Nasir is asking directly in PyMOL?



> On Feb 16, 2016, at 8:15 AM, Nasir Bashiruddin  wrote:
> 
> Hello! 
> 
> So, I've had this problem for a while now.
> 
> I have a ligand that goes deep into a protein.
> 
> I have the ligand with stick representation.
> 
> I have the protein in cartoon representation.
> 
> I have both ligand and protein surfaced with 0.5 transparencies.
> 
> The ligand surface is yellow and the protein surface is gray80.
> 
> The protein cartoon is set to transparency, 0.5 as well.
> 
> I want to show how the ligand goes deep into the binding site of the protein.
> 
> I can see the ligand surface going into the protein surface but when I Ray, 
> the yellow ligand surfaces that go into the protein disappear. 
> 
> How do I get the Ray quality and keep the ligand surface that is within the 
> protein from disappearing? 
> 
> Hope I explained this well.
> BTW, surface mode is set to 1 to include all atoms
> 
> Nasir
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Re: [PyMOL] surface properties

[H. Adam Steinberg]

Use my hydrophobicity script... Please build this in as preset as I use 
it all the time.


# Written by H. Adam Steinberg
# 08/22/2007
###set custom colors for each amino acid based on hydrophobicity scale 
(scale derived by S. D. Black and D. R.

Mould):
set_color ala, [0.525490196, 0.792156863, 0.596078431]
set_color arg, [0, 0.678431373, 0.9]
set_color asn, [0, 0.717647059, 0.8]
set_color asp, [0, 0.678431373, 0.9]
set_color cys, [0.584313725, 0.803921569, 0.560784314]
set_color gln, [0, 0.729411765, 0.760784314]
set_color glu, [0, 0.68627451, 0.894117647]
set_color gly, [0.470588235, 0.776470588, 0.631372549]
set_color his, [0, 0.694117647, 0.862745098]
set_color ile, [0.901960784, 0.898039216, 0.258823529]
set_color leu, [0.941176471, 0.91372549, 0.192156863]
set_color lys, [0.211764706, 0.741176471, 0.729411765]
set_color met, [0.698039216, 0.835294118, 0.48627451]
set_color phe, [1, 0.941176471, 0]
set_color pro, [0.643137255, 0.819607843, 0.525490196]
set_color ser, [0.321568627, 0.752941176, 0.698039216]
set_color thr, [0.4, 0.764705882, 0.7]
set_color trp, [0.803921569, 0.86667, 0.388235294]
set_color tyr, [0.854901961, 0.882352941, 0.325490196]
set_color val, [0.752941176, 0.854901961, 0.435294118]

###Select and select separate object for each amino acid:
select ala, resn ala
select arg, resn arg
select asn, resn asn
select asp, resn asp
select cys, resn cys
select gln, resn gln
select glu, resn glu
select gly, resn gly
select his, resn his
select ile, resn ile
select leu, resn leu
select lys, resn lys
select met, resn met
select phe, resn phe
select pro, resn pro
select ser, resn ser
select thr, resn thr
select trp, resn trp
select tyr, resn tyr
select val, resn val

###Color each amino acid with hydrophobicity color
color ala, ala
color arg, arg
color asn, asn
color asp, asp
color cys, cys
color gln, gln
color glu, glu
color gly, gly
color his, his
color ile, ile
color leu, leu
color lys, lys
color met, met
color phe, phe
color pro, pro
color ser, ser
color thr, thr
color trp, trp
color tyr, tyr
color val, val

###Show surface
show surface, all

DeLano Scientific wrote:

Mark,

PyMOL does not have such abilities at present.  


Can such concepts even be defined in a precise, objective, and unambiguous
fashion?  


Cheers,
Warren

--
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Subscriber Support Services
mailto:supp...@delsci.com

  

-Original Message-
From: Mark Collins [mailto:mnc2...@columbia.edu] 
Sent: Thursday, December 18, 2008 7:38 AM

To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] surface properties

Hi All
I have searched thru the archive and couldn't find an answer, 
to this.  I would like to make pymol surface(s) colored by 
(1) hydrophobicity and (2) concavity/convexity.
These are easily produced in grasp, so one possibility maybe 
to import some type of grasp file.

Thanks in advance for suggestions, websites, or tutorials, etc.
Mark

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Re: [PyMOL] incompletely drawn cartoon strands

[H. Adam Steinberg]

I just had the same problem, it seems to happen when parts of the 
cartoon from one of the objects overlaps with similar parts of a cartoon 
from the second object.


Daniel Rigden wrote:

Dear all

Thanks for the replies.  After a few minutes testing it seems that the
problem is only caused when I create an object which, unintentionally
(carelessly), selects from across different molecules.  If load 1jqd
through PDB loader then do

create parallel, resid 111-116 or resid 82-88 or resid 53-59 or resid
136-142

no problem.

However, if I make duplicate objects then issue the same create command
I see incomplete strands.  The artifacts are worse if there are two
duplicates than if there is one.

So, I don't know why this should PyMOL a problem, but the lesson seems
to be to take more care with object creation.  Incidentally, I could
also get round the problem by saving the object 'parallel' and reloading
it, but this workaround seems unnecessary.

Cheers

Daniel

On Thu, 2008-10-09 at 08:21 -0700, DeLano Scientific wrote:
  

Daniel,

This is just a guess, but I suspect that there is a problem with identifiers 
and/or residue ordering in the structure which may be confusing PyMOL.  A 
command like

label name ca, segi+"-"+chain+"-"+resi 


may help reveal what is going on.

Cheers,
Warren

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-Original Message-
From: Daniel Rigden [mailto:drig...@liverpool.ac.uk] 
Sent: Thursday, October 09, 2008 3:20 AM

To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] incompletely drawn cartoon strands

Dear all

I've just extracted a region of B sheet from a structure to produce a session 
for teaching purposes.  To my surprise, when I created an object from the four 
distinct stretches making up the sheet, PyMOL redrew the previously complete 
strands in a very incomplete way (attached).  When I colour by secondary 
structure I can see that they are all defined as 'beta'.  Why will cartoon not 
draw complete arrows for me?  I looked for settings that might be relevant but 
couldn't see any.  I'm on 0.99rc6, if that makes any difference.

Thanks in advance for your help

Daniel
 



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Re: [PyMOL] Using Pymol to View a Electrostatic Potential Energy Surface for an RNA-Protein Complex

[H. Adam Steinberg]

Would this work?
1. Make a copy to object of the protein, and make a separate copy to 
object of the RNA.

2. Apply a PES to the new protein obj.
2. Apply a PES to the new RNA obj.

Angelo Rossi wrote:

Hello:

I am trying to use pymol to view the pes for an RNA-Protein complex.

But, I want to use two different dx maps: one for RNA and one for the 
protein.


Here is what I did:

1) I read into pymol the pdb file for the entire RNA-protein complex.  
It looks good.


2) I then read in a protein.dx map hoping that it would overlap with 
the protein segment.  It didn't work.


Can someone please help me with this?

The reason for the two pes maps is that the RNA and protein have 
different characteristics, and I want to manipulate them separately.


Thanks for all your help in advance.

Kind regards,

Angelo


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Re: [PyMOL] Marking residues in a superposed diagram

[H. Adam Steinberg]

select resi 44 (or whatever residue number you'd like)

or

Click on Display in the menu at the top and click on Sequence On. All of 
your chains will appear at the top of the screen. Scroll the gray bar to 
the right and click on any of the residues you want to see.


Pankaj Barah wrote:

Hi,

I have a superposed 5 protein chains and now I have a superposed 
coordinate file. Now I want to mark few specific residues in the 
chains. How can I do that using pymol?


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Re: [PyMOL] PyMOL crashes under Vista Home Premium & Ubuntu 8.04 LTS

[H. Adam Steinberg]

One of my tricks is to only show part of the structure at a time, ray 
each part individually and the reassemble them in Photoshop. I do this 
all the time with the huge multi protein PyMol sessions I have to work 
on. It depends on your orientation in the viewer though, be careful to 
not cut anything off. With the ribo you can hide the large or the small 
subunit, render each separately, and then reassemble.


Michael Weber wrote:

Hi,
I have a problem when trying to ray 750,750 a quite large ribosome file 
with maximum quality. Size of the relevant PyMOL v1.1 file is 100 MB (or 
31 MB after reducing objects I do not need for the figure production). 
PyMOL simply crashes under Windows Vista Home Premium as well as under 
Ubuntu Linux v8.04 LTS without error report. My dual OS system is a 
Samsung Aura Seven Notebook (Core2Duo @2.4 GHz each, 3 GB of RAM, NVIDIA 
GeForce 9200M GS graphics board with 256 MB of RAM, 12" TFT @1280x800 
resolution settings). I first thought the RAM under Vista is still 
insufficient (Vista alone takes 900 MB of the 3 GB of memory) but then  
I realized that this crash occurs as well under Linux. However, since 
both OS are 32 bit and therefore to my (limited) knowledge cannot handle 
more than 2 GB in a single task, RAM limitation might still be an issue 
to think about, right?
I have experienced (and occasionally reported) this type of serious 
crashes with PyMOL on a broad variety of machines over some years now - 
usually occurring when trying to render final files - but, sadly, none 
of these has ever been diagnosed and fixed properly. Maybe this time I 
am lucky and someone knows what to do?

Best regards,
Michael.

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Re: [PyMOL] feature request

[H. Adam Steinberg]

It is especially difficult to remember which scene is which when you 
open a pse file that you haven't looked at for a few months. Would it be 
simple or easy to just let us name the scenes like we name the objects 
and selections in the pane on the right?


Sarina Bromberg wrote:
I find it difficult to keep track of all the scenes I create in a  
PyMOL session and where they are in the stack.  Would it be possible,  
at some point, to add a feature that displays numbered thumbnails of  
scenes in another window on the desktop?

Thanks,
Sarina
Sarina Bromberg
(650) 879-1492
PO Box 12, Pescadero, CA 94060
sarina.bromb...@att.net






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[PyMOL] nice DNA pdb and ring options

[H. Adam Steinberg]

I have three questions I'm hoping someone can help with.

1. Does anyone have, or can anyone point me to a program that will 
generate a nice pdb file that contains 50 or so base pairs of random 
sequence B form DNA with hydrogen bonds between the bases or no H bonds?


I need to be able to scultp the DNA and have one strand react to the 
pulling of the other strand. I also want to show the union of the AT and 
GC via H bonds. The H bonds can be regular bonds (and probably will have 
to be if I'm going to be sculpting). I can make the h bonds and make 
them real bonds for the sculpting, I'm just wondering of anyone has 
already done it or has a script around


2. When showing a cartoon of DNA the ribose ring in the backbone is 
always there no matter which setting you choose. How can I make the 
phosphates and the ribose rings show as a backbone cartoon "tube" and 
keep just the bases as filled sticks with rinngs?


3. Rings on DNA and RNA can be filled, in cartoon mode. But I can't get 
the rings to fill in on selected amino acids (H, W, Y, F) in a protein 
of that same file. Is there a fill amino acid ring setting?


Thanks in advance for anything you can offer,

Adam

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___________

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[PyMOL] Showing Si and Re faces

[H. Adam Steinberg]

Does anyone know how to show Re and Si faces of a backbone in PyMOL? I'm 
tired of putting them in by hand.

The Re and SI faces of a backbone are the "planes" that can be drawn by 
connecting the alpha carbon to the carbonyl oxygen to the next alpha 
carbon to the hydrogen of the nitrogen back to the 1st alpha carbon. 
These planes are what make up the strands and the alpha helices when you 
show a protein as "cartoon" in PyMOL.

Thanks in advance for any help!

Adam

-- 
_______

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<http://adam.steinbergs.us>

The Media Center
Department of Biochemistry
University of Wisconsin-Madison
433 Babcock Drive
Madison, WI 53706
608/265-4982
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Re: [PyMOL] Creating a single PDB from two PDB - ala docking by hand

[H. Adam Steinberg]

Bring up both pdb files in one session,
orient the ligand by going to editing mode and using the shift key with 
the left mouse button (3 button mouse mode) to move just the ligand.
Once you have it in the position you want,
type select all in the command line and then hit enter,
In the A menu for the (sele) you just created pick copy to object.
PyMOL will create a new pdb with all of the coordinates of the two pdb 
files as they are positioned on screen.
Rename it if you'd like, and save the new pdb out from the File 
menu/save molecule.


Mark Benson wrote:
> Dear All,
>
> I am trying to build a single PDB file from two different PDB 
> files.  One PDB has a small organic ligand, and the second PDB 
> contains amino acid side chains from an active site.
>
> I load both PDB files, but I want to "freeze" the orientation of 
> the amino acid side chains PDB ( not move it), and then place and 
> orient the ligand PDB in a certain pose with respect to the amino 
> acid side chains.
>
> Ideally, I would then like to save the coordinates for both the 
> amino side chains and the ligand coordinates to a single PDB 
> file.
>
> In the long run, I want to run a simple minimization on an 
> possible active site cluster and I want to get a feel for the 
> energetics of the ligand in the active site.  I don't like working 
> with MOLDEN or some of the other suites out there and I wanted to 
> try this with PyMOL.  I've gone through the manual, the web, 
> pymolwiki, the "masking" and "protecting" options, and I've tried 
> examining the use of frames and split_states, but I haven't come 
> up with anything.
>
> I've heard about a demo that Warren DeLano put on for the ACS 
> where, as part of the demo, he showed off some toy example where 
> he docked a ligand in by hand, complete with having PyMOL show 
> red/green dots for steric clashes/matches.
>
> Any ideas?
>
> -Mark
>
>
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[PyMOL] New MacPros and PyMOL - Radeon only?

[H. Adam Steinberg]

Hi All,

I bought a new MacPro and now get this message when I open PyMOL:

Note: Radeon HD cards tend not to run PyMOL well.
Use nVidia or Intel instead, if OpenGL glitches occur.
Attempting to compensate for known issues... 

So the new Macs only come with Radeon video cards... there are no other choices 
with a Mac. This means the MacPros no are no longer a good platform for running 
PyMOL? I just tossed $3K down the drain?

I tried to render the surface of 3L5Q and PyMOL just crashes (6GB RAM). I tried 
to render just the top half and it still crashes.

What are the OpenGL glitches that occur, are they documented somewhere?
What does PyMOL do to compensate?

I checked the PyMOL web site and under the supported operating systems and 
hardware there is no mention of the lack of Radeon support/poor Radeon 
performance. Maybe that should be added because I wouldn't have bought this new 
Mac if I would have known this. Is there anything I can do to make this new 
machine work?

I see a 64-bit version is on the horizon, will this address Radeon performance 
or should I go back to my old MacPro with it's nVidia 7300 video cards? 

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/729-5944

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[PyMOL] Morph DNA?

[H. Adam Steinberg]

Hi All,

I’m doing a number of morphs for a project and have one example that includes 
DNA.

I generated a second piece of straight DNA from scratch, and would like to show 
it morph into the protein bound DNA.

PyMol 1.8 doesn’t seem to want to morph DNA. It goes through the exercise but 
nothing is generated. Does it only work with proteins? Both nucleotides strings 
are ATOM (no HETEROATOM) and both are in the AGCT format, no DA DG DC DT format.

Does anyone know a program or web site that will morph DNA?

Thanks,

Adam
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Re: [PyMOL] query

[H. Adam Steinberg]

Scrolling the mouse will not move the molecule, it will reduce the fog that 
pymol puts in the image, making it less gray.

Sent from my iPhone

> On Apr 27, 2016, at 6:45 AM, ankita mehta  wrote:
> 
> No, I can not do this becos i have to show the complex that is protein in a 
> fix orientation.
> Suggest some alternative..
> Thanks!
> 
>> On Wed, Apr 27, 2016 at 4:01 PM, Dheeraj Prakaash  wrote:
>> Try pointing your (mouse) cursor in the Pymol Viewer and scrolling up and 
>> down! 
>> Usually (if you have not changed any settings), SCROLLING UP should solve 
>> your problem.
>> 
>> Cheers.
>> 
>>> On Wed, Apr 27, 2016 at 6:15 PM, ankita mehta  
>>> wrote:
>>> Hii,
>>> I want to save the image in pymol
>>> I am using white background but it gives me dull colouring of the protein 
>>> which is at the background than the protein part at foreground.
>>> I want a unified sceme for all protein .
>>> pls suggest.
>>> thanks!
>>> 
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[PyMOL] fix cartoon backbone

[h. adam steinberg]

Hi All,

I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. After I 
fixed those two breaks (add in the correct atoms and join them) how do I get 
the cartoon of the DNA to be complete? PyMOL still creates the cartoon with the 
breaks.

Thanks!

Adam

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Re: [PyMOL] fix cartoon backbone

[h. adam steinberg]

Thank you, that certainly brought the chains together, but sill no completed cartoon even after a rebuild.Attached is chain F, can you see anything wrong with this file that won’t let it display a complete chain? It must be with how I joined the missing atoms?I also notice that every time I open this object in PyMOL I get odd bonding happening. Even when I unbond those odd connections and resave the file, it puts them right back in when I reopen the file.I could simply fake the connection using photoshop, but I’m trying to learn to do it correctly! :) I appreciate your help!

chain F.cif
Description: Binary data
On Mar 22, 2019, at 11:31 AM, Jared Sampson <jared.samp...@columbia.edu> wrote:Hi Adam -The characters between the object names and the chain IDs are the segment IDs.  You can remove them by setting them to the empty string using `alter`:alter all, segi=""Hope that helps.Cheers,JaredOn March 22, 2019 at 12:14:46 PM, h. adam steinberg (h.adam.steinb...@gmail.com) wrote:On Mar 21, 2019, at 1:41 AM, Kevin Jude <kj...@stanford.edu> wrote:The DNA in 1CGP is made up of two annealed half sites, so there are four chain assignments for the two strands. If you want to display it as intact DNA, after adding the linking phosphate you can use the alter command to make the chains continuous. HTH.--Kevin Jude, PhDStructural Biology Research Specialist, Garcia LabHoward Hughes Medical InstituteStanford University School of MedicineBeckman B177, 279 Campus Drive, Stanford CA 94305Phone: (650) 723-6431On Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg <h.adam.steinb...@gmail.com> wrote:Hi All,I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. After I fixed those two breaks (add in the correct atoms and join them) how do I get the cartoon of the DNA to be complete? PyMOL still creates the cartoon with the breaks.Thanks!Adam___PyMOL-users mailing listArchives: http://www.mail-archive.com/pymol-users@lists.sourceforge.netUnsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe___
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Re: [PyMOL] fix cartoon backbone

[h. adam steinberg]

Thank you.

Interestingly…
These alter commands do work on the DNA in my original working .pse file, the 
file that contains all of the structures.
They do work on the “save molecule” as a cif file that I shared with you, if I 
open it into PyMOL by itself.
They also work if I open the chain F.cif into my original working .pse file. 
This will fix the new chain F but not the old chain F.

Something about saving the chain out as a cif file and bringing it back in 
alters something besides just the atom naming. 

> On Mar 22, 2019, at 1:43 PM, Thomas Holder  
> wrote:
> 
> Hi Adam,
> 
> The atom naming is nonstandard. If you fix that, the cartoon will be complete.
> 
> alter name P01, name="P"
> alter name O01, name="O5'"
> alter name O02, name="OP1"
> alter name O03, name="OP2"
> unbond name OP1, name O3'+O5'
> unbond name OP2, name O3'+O5'
> 
> PyMOL doesn't yet write bonds to mmCIF (it's on our TODO list, unfortunately 
> the mmCIF spec doesn't make this straight forward). You could save to MMTF 
> instead, it stores all bonds.
> 
> Cheers,
>  Thomas
> 
> 
>> On Mar 22, 2019, at 5:42 PM, h. adam steinberg  
>> wrote:
>> 
>> Thank you, that certainly brought the chains together, but sill no completed 
>> cartoon even after a rebuild.
>> 
>> Attached is chain F, can you see anything wrong with this file that won’t 
>> let it display a complete chain? It must be with how I joined the missing 
>> atoms?
>> 
>> I also notice that every time I open this object in PyMOL I get odd bonding 
>> happening. Even when I unbond those odd connections and resave the file, it 
>> puts them right back in when I reopen the file.
>> 
>> I could simply fake the connection using photoshop, but I’m trying to learn 
>> to do it correctly! :) I appreciate your help!
>> 
>> 
>> 
>>> On Mar 22, 2019, at 11:31 AM, Jared Sampson  
>>> wrote:
>>> 
>>> Hi Adam -
>>> 
>>> The characters between the object names and the chain IDs are the segment 
>>> IDs.  You can remove them by setting them to the empty string using `alter`:
>>> 
>>> alter all, segi=""
>>> 
>>> Hope that helps.
>>> 
>>> Cheers,
>>> Jared
>>> 
>>> 
>>> On March 22, 2019 at 12:14:46 PM, h. adam steinberg 
>>> (h.adam.steinb...@gmail.com) wrote:
>>> 
>>>> 
>>>> 
>>>>> On Mar 21, 2019, at 1:41 AM, Kevin Jude  wrote:
>>>>> 
>>>>> The DNA in 1CGP is made up of two annealed half sites, so there are four 
>>>>> chain assignments for the two strands. If you want to display it as 
>>>>> intact DNA, after adding the linking phosphate you can use the alter 
>>>>> command to make the chains continuous. HTH.
>>>>> 
>>>>> --
>>>>> Kevin Jude, PhD
>>>>> Structural Biology Research Specialist, Garcia Lab
>>>>> Howard Hughes Medical Institute
>>>>> Stanford University School of Medicine
>>>>> Beckman B177, 279 Campus Drive, Stanford CA 94305
>>>>> Phone: (650) 723-6431
>>>>> 
>>>>> On Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg 
>>>>>  wrote:
>>>>> Hi All,
>>>>> 
>>>>> I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. 
>>>>> After I fixed those two breaks (add in the correct atoms and join them) 
>>>>> how do I get the cartoon of the DNA to be complete? PyMOL still creates 
>>>>> the cartoon with the breaks.
>>>>> 
>>>>> Thanks!
>>>>> 
>>>>> Adam
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.

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Re: [PyMOL] Unwanted bond formed in azetidine ring

[h. adam steinberg]

Here is one way to do this:
change your mouse mode from “viewing” to “editing”.
left-click on the atoms at each end of the bond you wish to remove,
each atom will highlight with a gray ball around it,
In the command line type "unbond pkset” and hit the enter key,
your bond will be removed.

> On Jun 3, 2019, at 3:15 PM, Hao Li  wrote:
> 
> Dear users,
> 
> I am working on a structure of a protein-ligand complex, and the ligand 
> contains an azetidine group. Whenever I display this structure in pymol, an 
> unwanted bond forms between 2 carbon atoms in the azetidine ring. 
> 
> The pdb file of this ligand was generated by Chem3D and the restraint cif 
> file was generated by eLBOW in Phenix. I tried to edit both pdb and cif files 
> of the ligand but it did not work very well. I was able to remove certain 
> atoms but not the bond. 
> 
> I am kindly asking if there is a way to remove this unnecessary bond? Thank 
> you.
> 
> Regards,
> Hao
> 
> 
> 
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Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol?

[h. adam steinberg]

It’s the same command but just change the “S” to an “H”. Or you can use a “L” 
if you want a loop (unstructured).

alter 3-10/, ss=‘H’ 

You also need to enter the command: rebuild, to redraw the structure on your 
screen. Use rebuild after you enter the alter command.


> On Jun 4, 2019, at 10:37 PM, sunyeping via PyMOL-users 
>  wrote:
> 
> Dear pymol user,
> 
> I wonder why sometimes the secondary structure of a protein can not be 
> displayed incorrect in pymol. I have a structure, some residues are predicted 
> to be sheet or 3-10 helix with DSSP, but they are displayed as loop. Only 
> typing "dss" command in pymol doesn't work. I know by using the "alter" 
> commad the secondary structures can be assigned. The following command:
> 
> alter 61-63/, ss='S' 
> 
> can assign residue 61-63 as sheet. However, what is the command to assign 
> residues as 3-10 helix?
> 
> Thank you in advance.
> 
> Arthur
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Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol?

[h. adam steinberg]

When you use the alter command, then rebuild, and then save the PyMOL session 
as a .pse file, the changes will be written into the .pse file. They will not 
be lost when you reopen the .pse file.

The alter command doesn’t do anything to the actual .pdb or .cif file. It’s my 
understanding that when you open a structure file in PyMOL, it reads the pdb or 
cif file and then assigns appropriate secondary structure based on the phi and 
psi angles of the protein backbone.

> On Jun 5, 2019, at 11:50 PM, sunyeping  wrote:
> 
> Thank you for the reply.
> 
> Do alter and rebuild commands really change the secondary structure of the 
> specific residues or they just change the display? I saved the structure 
> altered bt the alter and rebuild commands, but when I open the structure 
> agian in pymol, the residues I changes are still displayed as in the original 
> structure file.
> 
> Best regards 
> --
> From:h. adam steinberg 
> Sent At:2019 Jun. 5 (Wed.) 20:43
> To:孙业平 ; pymol-users 
> Subject:Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol?
> 
> It’s the same command but just change the “S” to an “H”. Or you can use a “L” 
> if you want a loop (unstructured).
> 
> alter 3-10/, ss=‘H’ 
> 
> You also need to enter the command: rebuild, to redraw the structure on your 
> screen. Use rebuild after you enter the alter command.
> 
> 
> On Jun 4, 2019, at 10:37 PM, sunyeping via PyMOL-users 
>  > wrote:
> 
> Dear pymol user,
> 
> I wonder why sometimes the secondary structure of a protein can not be 
> displayed incorrect in pymol. I have a structure, some residues are predicted 
> to be sheet or 3-10 helix with DSSP, but they are displayed as loop. Only 
> typing "dss" command in pymol doesn't work. I know by using the "alter" 
> commad the secondary structures can be assigned. The following command:
> 
> alter 61-63/, ss='S' 
> 
> can assign residue 61-63 as sheet. However, what is the command to assign 
> residues as 3-10 helix?
> 
> Thank you in advance.
> 
> Arthur
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Re: [PyMOL] [EXTERNAL] broken DNA cartoon

[h. adam steinberg]

Thank you Blaine!

Now I know why, and how to manually fix this.

> On Mar 20, 2020, at 10:52 PM, Mooers, Blaine H.M. (HSC) 
>  wrote:
> 
> The O3' to P bond lengths are 2.2 Angstroms when they should 1.6 Angstroms.
> This is outside the bond length range that PyMOL accepts so the bond is 
> absent when you display the model as line or stick model.
> This is why the cartoon is missing or broken.
> 5FUR is a 8.5 Angstrom cryo EM structure.
> Perhaps the associated paper explains this discrepancy. 
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> 
> From: h. adam steinberg [h.adam.steinb...@gmail.com]
> Sent: Friday, March 20, 2020 8:57 PM
> To: pymol-users
> Subject: [EXTERNAL] [PyMOL] broken DNA cartoon
> 
> Hi All,
> 
> When I open 5FUR either from my drive or via fetch, the DNA cartoon is broken 
> and mostly missing (it should span from left to right). Any ideas on how to 
> get the cartoon to work?
> 
> Pymol version 2.3.4
> 
> 



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Re: [PyMOL] broken DNA cartoon

[h. adam steinberg]

Thank you Jared!

The commands didn’t work, but at least I now know why, and how to manually fix 
this.

> On Mar 20, 2020, at 10:37 PM, Jared Sampson  
> wrote:
> 
> Hi Adam - 
> 
> That's a fun one.  It appears that most of these O3' atoms are not bonded to 
> the P atom of the following nucleotide, which you can see if you show the DNA 
> chains as sticks.  Creating a bond via `bond atom1, atom2` results in a 
> normal cartoon.  Fortunately, the DNA chains are sequentially numbered, so 
> you can do something like:
> 
> for i in range(1, 80): cmd.bond(f"/5fur//E/{i}/O3'", f"/5fur//E/{i+1}/P")
> for i in range(81, 160): cmd.bond(f"/5fur//F/{i}/O3'", f"/5fur//F/{i+1}/P")
> 
> The offending bond lengths are much longer than a typical P–O bond, which is 
> why PyMOL's default distance-based bonding doesn't pick it up.
> 
> Hope that helps.
> 
> Cheers,
> Jared
> 
> 
> 
> From: h. adam steinberg  
> <mailto:h.adam.steinb...@gmail.com>
> Reply: h. adam steinberg  
> <mailto:h.adam.steinb...@gmail.com>
> Date: March 20, 2020 at 9:59:45 PM
> To: pymol-users  
> <mailto:pymol-users@lists.sourceforge.net>
> Subject:  [PyMOL] broken DNA cartoon 
> 
>> Hi All,
>> 
>> When I open 5FUR either from my drive or via fetch, the DNA cartoon is 
>> broken and mostly missing (it should span from left to right). Any ideas on 
>> how to get the cartoon to work?
>> 
>> Pymol version 2.3.4
>> 
>> 
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Re: [PyMOL] [EXTERNAL] Re: broken DNA cartoon

[h. adam steinberg]

Well, thank you very much Blaine! That worked great!

> On Mar 22, 2020, at 10:01 AM, Mooers, Blaine H.M. (HSC) 
>  wrote:
> 
> Hi Adam,
> 
> On my first attempt with Jared's commands, I pasted both for loops at the top 
> PyMOL prompt with a semicolon between the commands.
> This failed because I created a Python syntax error. 
> 
> When I issued Jared's commands one at a time, they worked.
> 
> Alternatively, rewrite Jared's for loops as list comprehensions.
> Now you can paste the two list comprehensions separated by a semicolon at the 
> PyMOL prompt.
> 
> [cmd.bond(f"/5fur//E/{i}/O3'", f"/5fur//E/{i+1}/P") for i in range(1, 80)]; 
> [cmd.bond(f"/5fur//F/{i}/O3'", f"/5fur//F/{i+1}/P") for i in range(81, 160)]
> 
> This worked for me. I am using PyMOL 2.3.4, the incentive product, but it 
> should work for older versions, even PyMOL 0.99.
> 
> You can issue many commands on one line if they are separated by semicolons. 
> There are some restrictions and limitations.
> For more details, https://github.com/MooersLab/EasyPyMOL and 
> https://www.ncbi.nlm.nih.gov/pubmed/27488983
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> 
> From: h. adam steinberg [h.adam.steinb...@gmail.com]
> Sent: Sunday, March 22, 2020 8:16 AM
> To: Jared Sampson
> Cc: pymol-users
> Subject: [EXTERNAL] Re: [PyMOL] broken DNA cartoon
> 
> Thank you Jared!
> 
> The commands didn’t work, but at least I now know why, and how to manually 
> fix this.
> 
> On Mar 20, 2020, at 10:37 PM, Jared Sampson 
> mailto:jared.samp...@columbia.edu>> wrote:
> 
> Hi Adam -
> 
> That's a fun one.  It appears that most of these O3' atoms are not bonded to 
> the P atom of the following nucleotide, which you can see if you show the DNA 
> chains as sticks.  Creating a bond via `bond atom1, atom2` results in a 
> normal cartoon.  Fortunately, the DNA chains are sequentially numbered, so 
> you can do something like:
> 
> for i in range(1, 80): cmd.bond(f"/5fur//E/{i}/O3'", f"/5fur//E/{i+1}/P")
> for i in range(81, 160): cmd.bond(f"/5fur//F/{i}/O3'", f"/5fur//F/{i+1}/P")
> 
> The offending bond lengths are much longer than a typical P–O bond, which is 
> why PyMOL's default distance-based bonding doesn't pick it up.
> 
> Hope that helps.
> 
> Cheers,
> Jared
> 
> 
> 
> From: h. adam steinberg 
> <mailto:h.adam.steinb...@gmail.com>
> Reply: h. adam steinberg 
> <mailto:h.adam.steinb...@gmail.com>
> Date: March 20, 2020 at 9:59:45 PM
> To: pymol-users 
> <mailto:pymol-users@lists.sourceforge.net>
> Subject:  [PyMOL] broken DNA cartoon
> 
> Hi All,
> 
> When I open 5FUR either from my drive or via fetch, the DNA cartoon is broken 
> and mostly missing (it should span from left to right). Any ideas on how to 
> get the cartoon to work?
> 
> Pymol version 2.3.4
> 
> 
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[PyMOL] incomplete secondary structure

[h. adam steinberg]

Hi all,

When I open 3jav the backbone shows many helices, but Pymol doesn’t draw them 
as helices when showing the cartoon. Clearly there is something that is not 
perfect with the deposited cyro structure.

If I run the dss command, the cartoon structure isn’t fixed, and I get repeats 
of the following error for each residue from 1-2750 for each chain: 
 AssignSS-Warning: Ignoring incomplete residue /3jav//D/2750  …

Does anyone know how I can fix the secondary structure without having to 
manually assign it to each helix?

Thanks!


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Re: [PyMOL] incomplete secondary structure

[h. adam steinberg]

Wow! I am always amazed at the level of knowledge on this list. Thank you both.

> On Apr 16, 2020, at 8:32 AM, Ali Kusay  wrote:
> 
> Hi Adam, 
>  
> As Annemarie has mentioned you will need a way of generating the backbone for 
> the regions in the structure that have simply been resolved as Ca atoms. 
> Another way to do this is to simple model 3jav on itself using modeller, 
> modeller can make a reasonable guess as to where helices should be based on 
> where the Ca atoms current are. This is quite simple to do and you can 
> construct all chains at the same time, however, without validation I would 
> only recommend using it for visualisation purposes, I have attached an image 
> of what the protein looks like after modelling if you are interested in 
> taking this route.
>  
> Cheers,
>  
> Ali
>  
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>  
> From: "honeg...@bioc.uzh.ch <mailto:honeg...@bioc.uzh.ch>" 
> mailto:honeg...@bioc.uzh.ch>>
> Date: Thursday, 16 April 2020 at 11:13 pm
> To: "pymol-users@lists.sourceforge.net 
> <mailto:pymol-users@lists.sourceforge.net>" 
> mailto:pymol-users@lists.sourceforge.net>>
> Subject: [PyMOL] incomplete secondary structure
>  
> When you look at the coordinate file for 3jav in a text editor, you'll see 
> that for the parts of the structure which give you a "AssignSS-Warning: 
> Ignoring incomplete residue" feedback, the coordinate file contains C-Alpha 
> coordinates only, while in the parts which render the secondary structure 
> properly, you have coordinates for all heavy atoms. The header contains 
> secondary structure information only for those residues where full 
> coordinates are available, and the dss command is unable to assign secondary 
> structure from C-Alpha only.
>  
> If you really want to obtain a cartoon representation for the whole molecule, 
> you either have to use a method to determine the secondary structure from 
> C-alpha atoms only, and assign the secondary structure to the molecule using 
> the "alter" command (laborious), or submit your coordinates to a server 
> capable of modelling a full atom structure from the Alpha trace (e.g. SABBAC 
> 1.3, 
> https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::SABBAC, 
> <https://protect-au.mimecast.com/s/1oetC0YKPvi46vD6uWIeGJ?domain=mobyle.rpbs.univ-paris-diderot.fr>
>  caution: you need to submit each chain separately, since the server cannot 
> deal with multi-chain models.
>  
> Annemarie
>  
> 
> Today's Topics:
> 
>1. incomplete secondary structure (h. adam steinberg)
> 
> 
> --
> 
> Message: 1
> Date: Wed, 15 Apr 2020 10:51:07 -0500
> From: "h. adam steinberg"  <mailto:h.adam.steinb...@gmail.com>>
> To: pymol-users  <mailto:pymol-users@lists.sourceforge.net>>
> Subject: [PyMOL] incomplete secondary structure
> Message-ID: <8b4fde28-444e-4f86-be2a-e2982eae4...@gmail.com 
> <mailto:8b4fde28-444e-4f86-be2a-e2982eae4...@gmail.com>>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi all,
> 
> When I open 3jav the backbone shows many helices, but Pymol doesn?t draw them 
> as helices when showing the cartoon. Clearly there is something that is not 
> perfect with the deposited cyro structure.
> 
> If I run the dss command, the cartoon structure isn?t fixed, and I get 
> repeats of the following error for each residue from 1-2750 for each chain: 
>  AssignSS-Warning: Ignoring incomplete residue /3jav//D/2750  ?
> 
> Does anyone know how I can fix the secondary structure without having to 
> manually assign it to each helix?
> 
> Thanks!
> 
> 
> Adam
> -- next part --
> An HTML attachment was scrubbed...
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> 
> 
> --
> 
> Subject: Digest Footer
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Re: [PyMOL] Outlines thickness

[h. adam steinberg]

I also use this feature for illustrations and would love to find a better way 
of controlling the outline thickness. Could anyone fill us in on the history of 
this feature?

In Chimera black outline is just a simple slider and it’s super easy to use. 
You just move the slider up and down and it shows you the black outline 
thickness without even having to render the image.

In PyMOL you can do a couple of things:
1. increasing the rendering size (more pixels in X and Y) will decrease the 
thickness of the black outline (and infilling).
Decreasing the rendering size will make the black outline thicker.
Note however that the detail/quality of the image is better with higher 
resolution and worse with lower resolution.

2. Change the ray_trace_gain. the default setting is 0.12.
Setting this to 1 will give you more black, but it’s not great (black infill is 
worse in many areas) and it depends on the resolution you choose in X and Y. 
Setting this to 0 will give you less black, but it’s not great (infill will be 
removed but so will many of the black outlines) and it depends on the 
resolution you choose in X and Y.  0.06 works fairly good at 1500dpi for less 
black and less infill.

3. Setting the Ray_trace_slope_factor higher, will also reduce the infill 
black. 0.9 Ray_trace_slope_factor and ray_trace_gain of 0.2 at 1500dpi looks 
fairly good.

It seems that PyMOL doesn’t have a way to easily control the ray traced black 
outline.

> On May 6, 2020, at 10:47 AM, Gianluca Tomasello  wrote:
> 
> Hi, 
> is there a proper way to increase outlines thickness in PyMol? 
> 
> I noticed that increasing ray_trace_gain setting outlines are drawn thicker 
> but increasing this setting increases also the number of outlines. 
> 
> Is there a way to increase thickness without increasing the outlines number? 
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Re: [PyMOL] Farewell

[H. Adam Steinberg]

Thank you Thomas for all the help you have provided us over the years! You have 
certainly made my experience with PyMOL far more useful and easier, with all of 
the answers and shortcuts you have provided to this list!

Adam


> On Apr 30, 2021, at 9:14 AM, Thomas Holder  
> wrote:
> 
> Dear PyMOL community -
> 
> The time has come for me to hand over my PyMOL development
> responsibilities at Schrödinger. It's been an incredible journey for
> me to get involved with the PyMOL community, to become a PyMOL fellow
> in 2011 and to start working full time for the project in 2012. I'm
> extremely grateful to all the people at Schrödinger who made this
> possible, and of course to all of you - the user community - who've
> shown me every day that my work is meaningful.
> 
> PyMOL has a unique place within Schrödinger, and a highly motivated
> and skilled team of developers and scientists stand behind it. They
> have some great plans and I'm excited to watch how they will take
> PyMOL to the next level.
> 
> I don't think that my PyMOL journey is over yet. But for the next
> chapter in my career, I'll "just" be a user and a member of the
> community. See you around.
> 
> Cheers,
>  Thomas
> 
> -- 
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> 
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Re: [PyMOL] Exporting data from PyMOL into OriginLab

[H. Adam Steinberg]

Hi Neena,

When you render out of PyMOL using the button (not the command line), it just 
renders out the view window. Therefore if you make the helix fill the entire 
viewport rectangle, you will effectively render out a ‘cropped” image.

If you turn on transparency (in the background setting), you will no longer 
have a background to worry about as PyMOL will render just the helix on 
transparency.

Adam

> On Jul 23, 2021, at 11:57 AM, Neena Susan Eappen  
> wrote:
> 
> Hello PyMOL users,
> 
> Let me clarify my question. Shown below is one example figure. There is no 
> way to crop any images on Origin graphing software. For this figure, I 
> cropped PyMOL peptide image files on word document and then inserted in 
> Origin graph. This is time consuming. 
> Is there a way to crop on PyMOL? 
> 
>  
> Any insight would be appreciated,
> 
> Thank you, Neena 
> 
> On Jul 22, 2021, at 5:43 PM, Neena Susan Eappen  > wrote:
> 
>> Hello PyMOL users,
>> 
>> I have some issues exporting images from PyMOL into a data analysis software 
>> called OriginLab (https://www.originlab.com/ ). 
>> If there is anyone in this mail list who integrates figures from PyMOL into 
>> Origin, please email me. I need some insights for data representation.
>> 
>> Many thanks,
>> Neena
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