Hi Jarrett,
Thank you very much for the fix, it works perfectly.
Best regards,
Istvan
On Wed, Jul 19, 2023 at 9:02 PM Jarrett Johnson <
jarrett.john...@schrodinger.com> wrote:
> Hi Istvan,
>
> I can reproduce the same issue. Seems to be some unintended behavior with
> how this multistate p
Hi Istvan,
I can reproduce the same issue. Seems to be some unintended behavior with
how this multistate pseudoatom object is created. I've attached a modified
center_of_mass.py script so that it should behave the way you expect. Let
me know if this works for you.
Example that I tried with this:
Hi,
I have a simulation trajectory loaded in Pymol and I want to display
certain interatomic distances interactively. This works perfectly fine with
normal atoms, I can see how these selected distances change over the course
of the simulation using the wizard and playing the movie. However, it see
You are right, thank you!
Cheers,
Enrico
чт, 27 янв. 2022 г. в 13:32, Ali Saad Kusay :
>
> Hi Enrico,
>
> I think it's because you are selecting side chains, glycine has no sidechain
> and alanine has single carbon atom side chain so this representation won't
> work for it. You would need to rem
Hi Enrico,
I think it's because you are selecting side chains, glycine has no sidechain
and alanine has single carbon atom side chain so this representation won't work
for it. You would need to remove the sidechains from the selection to make it
apply to the backbone atoms, i.e. cmd.select('re
additional question in the same field:
as I've mentioned before, before applying distance-based filtering, I
would like to change the representation of the lines to ball-and-stick
for the residues involved in the interactions:
cmd.select('rep lines and sidechain')
cmd.show_as('sticks', 'sele')
cmd.
Thank you very much, Ali!!
Cheers,
Enrico
чт, 27 янв. 2022 г. в 12:20, Ali Saad Kusay :
>
> Hi Enrico,
>
> You need to use the byres or br. Selection
> (https://pymolwiki.org/index.php/Selection_Algebra)
>
> I.e:
> cmd.select('br. (rep sticks & visible beyond 4 of not polymer)')
>
> Also, conside
Hi Enrico,
You need to use the byres or br. Selection
(https://pymolwiki.org/index.php/Selection_Algebra)
I.e:
cmd.select('br. (rep sticks & visible beyond 4 of not polymer)')
Also, consider hiding all protein residues and showing only the ones near the
protein, i.e.:
cmd.show('sticks','br. p
Dear Pymol Users!
I am working on the visualization of the protein-ligand contacts
identified using
preset.ligand_cartoon('pdb',_self=cmd)
Since the command also displays some residues, which are not involved
in the interactions (with the radicals located too far away) with the
ligand, I need to fi
Johnson; Pymol User list
Subject: Re: [PyMOL] distance
Hi Joseph,
Thanks for the example, I can reproduce it! Not sure if this should be
considered a bug, or just a misleading user interface. "involving side chains"
really means "side chains within selection". There are non
PhD
> Researcher
> Drew Lab
> Department of Biochemistry and Biophysics
> Stockholm University
> From: Joseph Brock
> Sent: Friday, 26 October 2018 8:57:44 AM
> To: Jarrett Johnson
> Cc: Pymol User list
> Subject: Re: [PyMOL] distance
>
> Thanks Jarrett! I will try that
8:57:44 AM
To: Jarrett Johnson
Cc: Pymol User list
Subject: Re: [PyMOL] distance
Thanks Jarrett! I will try that!
Cheers,
Joseph.
Joseph S. Brock | PhD
Researcher
Drew Lab
Department of Biochemistry and Biophysics
Stockholm University
From: Jarrett Johnson
Subject: Re: [PyMOL] distance
Built from source (github repo).
On Thu, Oct 25, 2018 at 5:56 PM Joseph Brock
mailto:joseph.br...@dbb.su.se>> wrote:
Hi Jarret,
Thanks for the reply!
Unfortunately so ;(
Did you build from source or install via apt-get?
https://pymolwiki.org/ind
nux_Install
>
>
> Cheers,
>
> Joseph.
>
>
>
> Joseph S. Brock | PhD
> Researcher
> Drew Lab
> Department of Biochemistry and Biophysics
> Stockholm University
> --
> *From:* Jarrett Johnson
> *Sent:* Thursday, 25 October 2018 11:34:
From: Jarrett Johnson
Sent: Thursday, 25 October 2018 11:34:28 PM
To: Joseph Brock
Cc: Pymol User list
Subject: Re: [PyMOL] distance
Hi Joseph,
I'm not able to replicate that on my end using open-source PyMOL 2.2 on Ubuntu
16.04. Does this behavior also occur for mole
Hi Joseph,
I'm not able to replicate that on my end using open-source PyMOL 2.2 on
Ubuntu 16.04. Does this behavior also occur for molecules fetched straight
from the PDB?
Jarrett J.
On Thu, Oct 25, 2018 at 4:44 PM Joseph Brock wrote:
> Hi pymol users,
>
>
> I've observed a weird behaviour wit
Hi pymol users,
I've observed a weird behaviour with the open source pymol (v 1.7.2.1-2.2
running on ubuntu 16.04).
When I try to create some distance objects either via the command line of the
actions menu, an object is created but no dashed lines appear. When I "zoom"
this object it is ver
nevermind, I was entering @distance.py instead of run distance.py
On Fri, Oct 13, 2017 at 2:05 PM, Leigh M wrote:
> Hi Jared-
>
> I just use the C-alpha xyz coordinates and use d = math.sqrt(dx**2 +
> dy**2 + dz**2).
> I've been using python alone without pymol...using your code with the
> pymol
Hi Jared-
I just use the C-alpha xyz coordinates and use d = math.sqrt(dx**2 + dy**2
+ dz**2).
I've been using python alone without pymol...using your code with the pymol
api works for individual distances but I'm calculating hundreds of
distances and need to write to a csv which does not seem to
Hi Leigh -
How are you getting the coordinates? This works for me:
```
import math
# Show more digits for the distance label
set label_distance_digits, 10
# Make an alanine residue
fab A, ala
# Get coordinates from 2 atoms
o = cmd.get_coords("/ala///1/O")[0]
h = cmd.get_coords("/ala///1/H")[
yep!
On Thu, Oct 12, 2017 at 2:07 PM, Roger Rowlett wrote:
> You are using d = sqrt(dx^2 + dy^2 + dz^2), right? (Where dx = x2 - x1,
> etc.)
>
> ___
> Roger S. Rowlett
> Gordon & Dorothy Kline Professor
> Department of Chemistry
> Colgate University
> 13 Oak D
You are using d = sqrt(dx^2 + dy^2 + dz^2), right? (Where dx = x2 - x1,
etc.)
___
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-2
Anyone know how pymol calculates distance between two atoms?
I wrote a python script that calculates distance using the distance formula
and the xyz coordinates in the pdb, and it differs from the wizard by ~40%.
Any ideas on what might be going on would be helpdul
Thanks!
Leigh
-
Hi Thomas,
now I have the label visible immediately (w/o using ray)!
Thank you very much!
Burkhard.
On 02/28/2014 04:54 AM, Thomas Holder wrote:
> Hi Burkhard,
>
> bug fixed in SVN rev 4067. Let me know if it works for you.
>
> Cheers,
> Thomas
>
> On 27 Feb 2014, at 10:07, Thomas Holder wro
Hi Burkhard,
bug fixed in SVN rev 4067. Let me know if it works for you.
Cheers,
Thomas
On 27 Feb 2014, at 10:07, Thomas Holder wrote:
> Hi Burkhard,
>
> this was a very strange ATI only bug which we already could fix in our
> Incentive PyMOL release. The fix should soon make it into the o
Hi Burkhard,
this was a very strange ATI only bug which we already could fix in our
Incentive PyMOL release. The fix should soon make it into the open-source
version as well.
Thomas
On 26 Feb 2014, at 02:30, endew...@prisner.de wrote:
> Dear PyMOL Experts,
> I did check on the mailing list an
Dear PyMOL Experts,
I did check on the mailing list and fond one email about my problem but it
seems it was nor resolved:
(http://sourceforge.net/p/pymol/mailman/message/31119931/)
I use PyMol : PyMOL(TM) Molecular Graphics System, Version 1.7.0.0.
and have the problem that the distance command
Hi Mehdi,
use the distance command:
http://pymolwiki.org/index.php/Distance
Example:
PyMOL> distance cAB, chain A, chain B, 6.0
Hope that helps.
Cheers,
Thomas
Mehdi Talebzadeh Farooji wrote, On 04/19/13 21:49:
> Dear Pymol Users,
>
> I was wondering if there is a way to sh
Dear Pymol Users,
I was wondering if there is a way to show distances between two objects (two
chains) and filter them; for instance to display distnaces between atomes of
two interacting protein chains which are less than 6 A.
Any help would be much appreciated,
Mehdi
Thanks Thomas!
I've already tried use this command.
I want just ask about Hbond representation between 2 selected regions.
E.g I want to represent Hbonds beetween 2 helices
Firstly I've added donor Hydrogens
H_add donors
and than
distance 3sn6 and resi 197-220, 3sn6 and resi 275-298, cutoff
Hi James,
use the distance command:
http://pymolwiki.org/index.php/Distance
For the potential h-bonds, use it with mode=2.
Cheers,
Thomas
On 01/24/2012 05:15 PM, James Starlight wrote:
> Dear PyMol Users!
>
> In the PyMol Wizard I've found very userful option called distance
> measurements b
Dear PyMol Users!
In the PyMol Wizard I've found very userful option called distance
measurements beyween selected atoms.
I wounder to know how I could realize such operation via PyMol console in
the simplest manner.
My current task consist of making different point mutations and subsiquent
qu
Ah, indeed, the latest revision 3969 has a correctly working distance
command.
Thanks Jason.
Andreas
On 29/09/2011 3:08, Jason Vertrees wrote:
> Hi Andreas,
>
> It was a bug with the invalidation system. I just pushed a fix to source
> forge.
>
> Thanks for bringing this to our attention.
>
Hi Andreas,
It was a bug with the invalidation system. I just pushed a fix to source forge.
Thanks for bringing this to our attention.
Cheers,
-- Jason
2011/9/29 Andreas Förster :
> Hi all,
>
> Has anyone noticed that the distance command behaves oddly. Has this
> been recently introduced?
>
Hi,
My pymol 1.4.1 works fine.
can you try to ray trace and see if your objects are available but just not
displayed on the standard screen?
cheers,
2011/9/29 Andreas Förster
> Hi all,
>
> Has anyone noticed that the distance command behaves oddly. Has this
> been recently introduced?
>
>
O, and just when I pressed send (which also made firefox crash for
some reason), it struck me that you only load files, which means that
you're only appending states. But you don't specify a state to
calculate the distance, which means the first is taken again and
again. You might want to add a lin
Hi pkb bioinfo (which I do hope is not your real name),
Did you actually paste the script or did you retype it?
> from pymol import cmd
> from glob import glob
>
> lst = glob("*.pdb")
> lst.sort()
>
> for fil in lst:
> cmd.load(fil,"tmp")
> dst=cmd.distance('/tmp//A/LYS`203/NZ','/
Hello Pymol users,
I am new to pymol scripting and I want to calculate the distance between two
points of all the pdb file in a directory.
I tried to write the script but seems its not working.
PLease help me.
from pymol import cmd
from glob import glob
lst = glob("*.pdb")
lst.sort()
for fil in
Hi all
I have to measure a distance between one atom in one molecule
(object) and second atom in many molecules (objects) - to do so
interactively there is no problem:
distance MODEL1//A/211/CA , ManyMODELS_*///100/CA.
How can I write a script that will help to get the list of the
distan
It works,
thanks
Quoting Toni Pizà :
Try with the command
hide labels
--
"Two of the most famous products of Berkeley are LSD and Unix. I don't
think that this is a coincidence."
http://servomac.blogspot.com
Try with the command
hide labels
--
"Two of the most famous products of Berkeley are LSD and Unix. I don't
think that this is a coincidence."
http://servomac.blogspot.com
Hi,
I just calculate the distances between atoms in proteins with the function
'distance selection1, selection2'. As I want to generate a picture
with the distances of interest my question is:
is there any way to NOT visualise the distance number on my protein
but just keep the dotted line con
set_name oldname, newname
On Feb 12, 2008 2:48 PM, Toni Pizà wrote:
> > An object whose name begins with an underscore will not appear in the
> menu.
>
> Perfect! But how can I change the name of one name in the Names Panel?
>
> --
> "Two of the most famous products of Berkeley are LSD and Unix.
> An object whose name begins with an underscore will not appear in the menu.
Perfect! But how can I change the name of one name in the Names Panel?
--
"Two of the most famous products of Berkeley are LSD and Unix. I don't
think that this is a coincidence."
http://servomac.blogspot.com
An object whose name begins with an underscore will not appear in the menu.
On Feb 11, 2008 3:13 PM, Toni Pizà wrote:
> Hi!
>
> When I create a distance in a pymol session, an object called "dist n"
> is created, and a label with there name is shown at the right of the
> screen, with the other ob
Hi!
When I create a distance in a pymol session, an object called "dist n"
is created, and a label with there name is shown at the right of the
screen, with the other objects loadeds. Can I create a dist, and
render the dotted line at the screen, without having the label in the
right menú?
Thanks
On Monday 21 January 2008 23:51:15 Toni Pizà wrote:
> > I'm not sure this is what you're asking, but I use scripts by typing:
> >
> > @script.pml
>
> Thanks for your response, but I'm asking how to pass arguments to
> pymol's scripts written in Python. I type "run nameOfScript.py" within
> pymol fo
> I'm not sure this is what you're asking, but I use scripts by typing:
>
> @script.pml
Thanks for your response, but I'm asking how to pass arguments to
pymol's scripts written in Python. I type "run nameOfScript.py" within
pymol for this, but I would pass some arguments, such as "run
script.py a
Hi guys!
I hope you enjoy your time with Pymol, it's so nice ;)
I have a few doubts; anybody know if it's possible to change the color
of the dotted line drawn by the distance command?
How can I pass an argument to a python script run with "run script.py"?
Thank you!
Hi pymol users,
I want to create a pdb file that contains two polypeptide molecules. And
create a distance between them, i.e move one relative to the other. Can i do
this in Pymol?
Please i'll appreciate any help with this.
Regards
John
_
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf
> Of gilleain torrance
> Sent: Friday, February 23, 2007 2:16 PM
> To: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Distance Label Format
>
> Hi,
>
> Hmm. Not very easily. The measurement wizard just calls a
&g
Hi,
Hmm. Not very easily. The measurement wizard just calls a distance
method, which makes the dashed line and the label internally. Other
wise it would be simple to say:
cmd.label_dash("%0.1f" % d)
assuming that there was such a command... :) Oh, and that command
would need a dash object as a
Hi Folks,
When using the distance wizard is there a way to change the number of
decimal places output to the label from 2 to 1?
Thanks,
Tony
Anthony A. Armstrong
Department of Biophysics and Biophysical Chemistry
Johns Hopkins University School of Medicine
725 North Wolfe Street
Baltimore, MD 21
I needed to have a measurement of the "actual" physical long dimension of a
protein model to compare with x-ray scattering data. I activated the surface
mesh feature and at the extreme ends of the longest axis, right at the
surface boundary, created a carbon atom at each position, then simply u
Hi Giacomo,
you can either create an atom at that position
(see eg. http://www.rubor.de/bioinf/tips_python.html#chempy) and than
use the distance command (or wizard).
Or you can get the position of your first atom and simply calculate the
distance of the two positions,
sth. like:
class MyAt
Dear Pymol users,
I would like to measure the distance between an atom and
a specific point (not another atom) in the surface of the protein.
Is it possible with pymol?
do I need additional scripts?
Thanks in advance,
Giacomo Bastianelli
Hi,
I just downloaded a PyMOL v0.98 standalone executable and have it
running under Mandrake linux 10. I just noticed that the distance wizard
does not show the actual distance labels. Does anybody know how to turn
these on?
Thanks,
Anton Vila
rs-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Gareth Stockwell
Sent: 24 May 2005 10:44
To: Grégori Gerebtzoff
Cc: 'Sara Nichols'; pymol-users
Subject: RE: [PyMOL] distance between aromatic residues
On Tue, 2005-05-24 at 11:34 +0200, Grégori Gerebt
On Tue, 2005-05-24 at 11:34 +0200, Grégori Gerebtzoff wrote:
> 3) define two interlaced loops and calculate the distance between all 6
> carbons of Phe1 with all 6 carbons of Phe2, either with cmd.dist or with
> simple mathematical functions; sum these distances
>
> 4) divide the result by 36, and
Hi Sara,
I don't think this is directly possible, since the centers of the aromatic
rings are not declared per se. But I see another way to obtain the result
you want, maybe this can be written as a small Python script (sorry I never
wrote any Python scripts, so I can't translate my idea!!).
The i
Hi List,
I was wondering if anyone knew of a way to set a distance measurment
between two aromatic rings, where the distance is measured from the
center of the ring, rather than a specific atom.
thanks
Sara Nichols
Gareth Stockwell wrote:
Hi Kristl,
I'm not sure if PyMOL can do it, but it's not too hard to do a bit of
vector algebra which gives the answer.
Let the coordinates of the nitrogens be A, B, C, D, and the iron atom F.
Compute the centre of your nitrogens:
X = (A + B + C + D) / 4
Then you wor
Hi Kristl,
I'm not sure if PyMOL can do it, but it's not too hard to do a bit of
vector algebra which gives the answer.
Let the coordinates of the nitrogens be A, B, C, D, and the iron atom F.
Compute the centre of your nitrogens:
X = (A + B + C + D) / 4
Then you work out a normal to the plan
Hi Pymolers!
Is there a way for me to define a plane of atoms say 4 Nitrogens in a heme
complex and then determine how far out-of-plane the Fe atom is? If so
either in Pymol or another program I'd love to know the secret.
Thanks,
Kristl
kri...@physics.purdue.edu
> From: Jules Jacobsen [mailto:jo...@hermes.cam.ac.uk]
>
>
> you can change most of the parameters using set dash_n where
> n= length,
> width, gap, radius. Unfortunately dash_color doesn't exist.
>
...but you can change the color of a distance object
color red,dist01
Warren
you can change most of the parameters using set dash_n where n= length,
width, gap, radius. Unfortunately dash_color doesn't exist.
hope this helps
Jules
On Tue, 22 Oct 2002, franck coste wrote:
> Hi,
> I'd like to know if it's possible to change the parameters of the
> DISTANCE command (color,
Hi,
I'd like to know if it's possible to change the parameters of the
DISTANCE command (color, radius, ...)
Thanks,
Franck Coste.
> From: Kristian Rother
> In this and other recent questions inside and outside this
> forum i have
> discovered that many of them could be solved quite easy if
> there was an
> easy way to access the atomic coordinates directly from the PyMOL API.
>
> Is this achievable somehow?
The actual
Yuuki,
I've glanced at the code and found that there's no way to get that
information out directly right now. The dist command only returns the
average distance drawn -- this is because a single distance command can be
used to draw distances to many atoms. To accomplish your goal, you would
n
Hi all,
I'm making sequenced pictures to be a movie. Each picture
contains distance between atoms, and I can SEE them changing in
the movie. Does someone know whether PyMol can output this sequenced
atom distance to a file, and how? Normal text format will be O.K.
Thanks a lot.
Yuuki
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