[PyMOL] electron density in plane

basically a (flat) surface with different colours. Any pointers would be appreciated. -- Groeten, David. Dr. David van der Spoel,Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala

[PyMOL] surfaces

the objects. The menus do not let me change colors either. I presume pymol doesn't regard these triangles as "surfaces". Is there any way to make compiled graphics object transparent? Or to create surfaces in another way than using cgo's?

[PyMOL] transparent CGOs?

Hi, a rephrase of my earlier question: (how do/can) I make my CGO's transparent? Isn't it simply a property of the OpenGL object? -- Groeten, David. ____ Dr. David van der Spoel,Biomedical center, Dept. of Bi

[PyMOL] accessing objects directly

Hi, How do I access the objects I load from files (e.g. pdb file) directly (i.e. in a script)? If I want to print the coordinates of an atom, or the value of at a point in the electron density grid? -- Groeten, David. Dr

Re: [PyMOL] Show Sticks - Turns Molecule Blue

Assuming you're using a recent version of openSUSE (11.3, 11.4, or Factory), feel free to grab the svn compiled version from http://software.opensuse.org/download.html?project=devel:languages:python&package=pymol -David 2011/9/11 Troels Emtekær Linnet : > This should get you o

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

the builds on https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython for opensuse 11.3 and 11.4 use gcc4.5 successfully. I blame ubuntu or linux mint. -David On Dec 2, 2011, at 10:21 AM, Marius Retegan wrote: > Could you please specified what exactly

Re: [PyMOL] Using super correctly

-1 and for super, the default value was 0. -David On Fri, Jan 13, 2012 at 7:44 AM, QT wrote: > Dear all, > > I'm having a tough time using the super command correctly.  I want to > superimpose two 5S structures. > > In pymol, I'll do the following > > load 2awb.pd

Re: [PyMOL] cmd.do(png filename) error

; > > but, if I execute the following script, the png file does not arise: > > from pymol import cmd > cmd.do('load tmp.pdb, tmp') > cmd.do('png tmp.png') > > No any error is reported on pymol console. Can you try do

Re: [PyMOL] Using super correctly

n complains to you about "invalid selections" because it thinks the selections are empty. -David On Fri, Jan 13, 2012 at 8:37 AM, David Hall wrote: > I think super does not handle nucleic acid sequences well. > > super ec-5s, hm-5s, seq=-1 > > works. > > I'll l

Re: [PyMOL] Open Source PyMOL v1.5.0.1

http://software.opensuse.org/download.html?project=devel:languages:python&package=pymol and choosing the appropriate openSUSE release and architecture. -David -- Keep Your Developer Skills Current with LearnDevN

Re: [PyMOL] Little coordinate cross in Pymol?

http://pymolwiki.org/index.php/Axes -David On Feb 27, 2012, at 5:38 AM, Gudrun Lotze wrote: > Dear all, > > is it possible to show in Pymol a little coordinate cross with axes x,y,z, > for example like in VMD, please? > I have a protein made from dummy atoms and there is no

Re: [PyMOL] Editing of the pdb structure

ct9.html#TER ) Chain breaks in crystal structures are generally not the carboxy-terminal residues. -David -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click

Re: [PyMOL] GUI to improve interaction between user and PyMOL

by browsing the pymolwiki that also use graphical elements and may also be helpful. -David On Thu, Mar 22, 2012 at 4:39 PM, Suhaila Haji Mohd Hussin wrote: > Hello everyone. > > Is there any useful online reference that can be shared for me to learn how > to add GUI executed by Python s

Re: [PyMOL] Is there or should there be a pymol annotation server?

The main technology I've seen used for interactive publications is ActiveICM (see http://www.molsoft.com/activeicm.html#aipub ). In my lab, we regularly include pymol sessions as supplementary material to help people understand our results. -David On Friday, July 13, 2012 at 6:41 AM, T

[PyMOL] Pymol Rotated Screen

, the same thing happens. Interestingly, while the desktop background and any app on the screens are impacted, the mouse cursor is not. Note, the incentive build PyMolX11Hybrid does not have this problem. Thanks for any help, David Hall

[PyMOL] question about biological units, states, etc.

Hello, all. First let me announce that I am not a PyMOL poweruser, and I have virtually no experience with crystallography and its data files. I have been plugging along using the PyMOLwiki as my knowledge-base for years, but cannot seem to wrap my head around certain issues. For example, 6pfk

Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a "test" pdb.

You don't need a license for the open source version. If you provided details on what OS/distribution you are building on, people may try to replicate and understand why the python version hung. In my experience, using setup.py generally worked out of the box. -David On Oct 4, 2012, at

Re: [PyMOL] How to rotate entire section of structure relative to rest

If you are comfortable with the command line interface, you can use http://pymolwiki.org/index.php/Set_Dihedral -- David Hall On Monday, October 22, 2012 at 4:27 PM, Alex Truong wrote: > Hi All, > > I'm relatively new to this software, and even though I've been using it

Re: [PyMOL] Custom menus and shortcuts?

http://pymolwiki.org/index.php/Set_Key http://pymolwiki.org/index.php/Extend is also useful. -David On Tuesday, October 23, 2012 at 6:02 AM, Boris Kheyfets wrote: > Hello PyMOL users, > > Menus > = > > Is there a way I can add custom menu in PyMOL? > > Ideall

Re: [PyMOL] iPad pymol questions

on in the upper right corner, since the dropbox app has cached them locally, PyMol just reads the file and doesn't need the internet -David On Wed, Nov 28, 2012 at 11:48 AM, Steve Williams wrote: > I am a new subscriber to the pymol listserv. I did look around a bit on the > listserv s

Re: [PyMOL] How to hide the object control panel

http://pymolwiki.org/index.php/Internal_gui -David On Sunday, March 24, 2013 at 7:54 PM, Matthias Haffke wrote: > Dear all, > > this might be a simple question, but I would like to know how to hide the > object control panel on the right side in the PyMol window. > I would

Re: [PyMOL] PyMOL 1.6 pre-release announcement

beta test can use devel:languages:python repo in openSUSE: https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython -David On Sun, Mar 24, 2013 at 6:02 AM, Thomas Holder wrote: > Dear PyMOL users, > > The pre-release version of PyMOL 1.6 has been

Re: [PyMOL] Pymol error in Mac OS X 10.8.2

what method did you use for installation? -- David Hall On Wednesday, May 1, 2013 at 11:53 AM, Rhitankar Pal wrote: > I am having some issues after installing pymol in Mac OS 10.8.2. It seems > the program is installed but when I try to open in using command line > "pymol&qu

Re: [PyMOL] Pymol error

by default, macports installs tcl with the +corefoundation variant (see http://guide.macports.org/#using.variants ) if you do: sudo port install tcl -corefoundation that will solve the problem. -David On Mon, May 6, 2013 at 8:26 PM, Rhitankar Pal wrote: > Dear Thomas, > >

Re: [PyMOL] Pymol error

sudo port install tk -quartz It has nothing to do with what OS X ships with, it has to do with current macports defaults, which changed around 18 months ago. You can dig around the macports bug reports to see discussion of the change. -David On Tue, May 7, 2013 at 1:32 PM, Rhitankar Pal wrote

Re: [PyMOL] PyMOL 1.6 pre-release announcement

pymol 1.6 as I cannot share sessions with them (at least not without getting weird e-mails asking why I have a sudden affinity for the color red). -David On Tue, Jun 18, 2013 at 7:37 AM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > This is fixed in SVN rev 4032. &

Re: [PyMOL] Pymol Library Script: findSurfaceResidues

provide more details on how you made your file, people may be able to tell you how to avoid the problem. -David On Saturday, July 13, 2013 at 9:31 AM, Muhtari Adanan wrote: > > > > Dear Group, > > > > I am a complete novice, thus hoped you would provide guidance on

[PyMOL] Pymol and load_traj

taken from VMD). The issue occurred as for my first attempts at loading a trajectory I was attempting to select a small portion using the start and stop options. Are there known issues with load_traj - I was not able to find any hints using Google. Thanks David

Re: [PyMOL] Leap motion control

Jason can fill you in if there's an update, but the latest status update I'm aware of was: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11572.html -David -David On Monday, July 29, 2013 at 11:04 AM, H. Adam Steinberg wrote: > It would be great if we could

Re: [PyMOL] How to move/turn CGO

For a definition of TTT , see http://pymolwiki.org/index.php/Object_Matrix You'll notice that set_object_ttt takes a 16-member list that corresponds to this matrix. -David On Aug 12, 2013, at 11:48 AM, Павел Томашевский wrote: > Thank you Thomas, translate and rotate works great, but

Re: [PyMOL] using pymol commands in a script

as line numbers. There are many text editors that do so. One with syntax highlighting for python would also be useful as it will make many of the issues much more apparent. -David On Wed, Sep 4, 2013 at 3:30 AM, Anasuya Dighe wrote: > Hi everyone, > > How to write PyMol commands in

Re: [PyMOL] Trouble with saving mol2 format

One feature request, it would be nice if I open a mol2 and then save that molecule as mol2, it would remember the atom types and charges. No need for assignment, just remember what the user read in. -David On Thu, Sep 19, 2013 at 1:03 PM, Thomas Holder < thomas.hol...@schrodinger.com>

[PyMOL] How to pass a list of selections into pymol script

.. I get an error that my_module expects only one argument. It has been suggested that I pass a list of strings and then access the selections based on the string name of the selections, however, I have not been able to find the

[PyMOL] Error loading pymol libraries from a python script.

Dear PyMOL Users, I am trying to run some pymol functions from a python script. For simplicity purposes, the script is called "script.py" and it's as simple as this : #cat script.py import pymol # Then I run it like this : #export PYMOL_PATH=/opt/soft/pymol-v1.5.0.3 #export PYTHONPATH=/opt/soft

Re: [PyMOL] Error loading pymol libraries from a python script.

Yes! This has worked. Thanks Thomas. 2013/12/5 Thomas Holder > Hi David, > > incentive pymol builds have the python interpreter and the _cmd module > built into the pymol.exe executable. This means running the script with > your system python is not supported. Instead, run y

Re: [PyMOL] Still need help with fetch and pymol 1.7

so on. Then the code will skip the entries in the windows registry that are causing issues. -David On Mon, Jan 20, 2014 at 8:40 AM, Lapolla, Suzanne M (HSC) < suzanne-lapo...@ouhsc.edu> wrote: > I am posting this again as I have still not figured out why I am unable to > fetch or use

Re: [PyMOL] Color starting midway between adjacent chains

set_bond line_color, color_name, n. CA+CB will color all bonds between CA and CB whatever color you put in as color_name If you're doing sticks instead of lines, you should use set_bond stick_color, color_name, n. CA+CB -David On Mon, Mar 3, 2014 at 10:01 PM, I-Ji Jung wrote:

[PyMOL] noInvalidateMMStereoAndTextType flag

displayed. I just cant figure out what this was supposed to be doing - it just doesnt seem right that input data of this type is being clobbered. Thanks for any info David -- Learn Graph Databases - Download FREE O'Reilly

Re: [PyMOL] noInvalidateMMStereoAndTextType flag

On Sun, Mar 23, 2014 at 06:02:32PM -0400, Thomas Holder wrote: > Hi David, > > very well analyzed. You are right that noInvalidateMMStereoAndTextType should > never be set to 0 in the open-source version, we will fix that. > > FYI: The incentive version of PyMOL can

Re: [PyMOL] noInvalidateMMStereoAndTextType flag

Not sure if the git svn stopping at rev 3938 was a question, but maybe you are using the old svn URL? svn://svn.code.sf.net/p/pymol/code/ Should get you up to date -David > On Mar 23, 2014, at 10:18 PM, David Osguthorpe > wrote: > >> On Sun, Mar 23, 2014 at 06:02:32PM -0400

Re: [PyMOL] noInvalidateMMStereoAndTextType flag

On Mon, Mar 24, 2014 at 05:46:15AM -0400, David Hall wrote: > Not sure if the git svn stopping at rev 3938 was a question, but maybe you > are using the old svn URL? > > svn://svn.code.sf.net/p/pymol/code/ > Sorry - I was unclear - I did not mean the revisions stopped th

Re: [PyMOL] Pymol wrl output

Have you tried doing show > as > surface It appears the wrl file has a bunch of extra information from the cartoon representation, which could confuse shapeways? -David On Sun, May 4, 2014 at 4:49 AM, Grateful Frog wrote: > Hi Jared & everyone, > > First, thanks for all

Re: [PyMOL] Pymol wrl output

ops out another menu where you can choose representations. -David On Sun, May 4, 2014 at 8:40 AM, Grateful Frog wrote: > HI David, > > Thanks for that tip. I didn't understand where the menu show > as > > surface is? > > But, I did "Hide everything", t

Re: [PyMOL] Access to pymol commands from the terminal

(sed '1d' protein.pdb; sed '1d' lipid.pdb) > merged.pdb --or-- tail -q -n '+2' protein.pdb lipid.pdb > merged.pdb -David On Thu, Sep 4, 2014 at 6:19 AM, James Starlight wrote: > Hi Tsjerk, > > Thanks alot! > Also I have the task to merge pro

Re: [PyMOL] need help

mand ( http://www.pymolwiki.org/index.php/Load ) -David On Tue, Sep 9, 2014 at 9:52 AM, Vic Pinas wrote: > Dear all, > > I need help. > > I just start using Pymol in Ubuntu, this was advised to me since windows > give a lot of trouble. > > I install pymol already on ubuntu, bu

Re: [PyMOL] Help with rms_cur command

almost definitely is http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg1.html -David On Mon, Oct 6, 2014 at 12:17 PM, Soisson, Stephen M < stephen_sois...@merck.com> wrote: > Hi everyone- > > > > I’m having a few issues with the rms_cur command that I am

Re: [PyMOL] CONECT table

http://www.pymolwiki.org/index.php/Connect_mode -David > On Oct 6, 2014, at 6:35 PM, Markus Heller wrote: > > Hello, > > How can I get PYMOL to use the CONECT table from a PDB file? My protein is > glycosylated, and I'd like to properly and automatically display the

[PyMOL] colour surface meshes

Hi all Is pymol able to save surface mesh files (.obj or .wrl) which include face colours? Many thanks David ___ David J. Pattinson PhD Student in the Centre for Pathogen Evolution Department of Zoology University of Cambridge dj...@cam.ac.uk

Re: [PyMOL] select state not working

I'm a little confused by what PDB assemblies you are talking about that are distributed as multi-state structures, but assuming they are similar to NMR models... you can use intra_fit ( http://www.pymolwiki.org/index.php/Intra_fit ) For example, with 2kgx, we start out with chain a in state 1 and

Re: [PyMOL] Is it possible to move different subunits independently using Pymol

also http://www.pymolwiki.org/index.php/Transform_selection and PyMOL>help rotate DESCRIPTION "rotate" rotates the atomic coordinates of atoms in a selection about an axis. Alternatively, it modifies the matrix associated with a particular object or object state. USAGE rotate

Re: [PyMOL] DNA representation

colored by chain set cartoon_ladder_radius, 2 set cartoon_tube_radius, 2 set ray_trace_mode, 1 -David > On Dec 13, 2014, at 1:22 AM, Jacob Lewis wrote: > > Hi, > > Does anyone know how to show DNA like this in pymol? > >

Re: [PyMOL] CGOs

where are you getting this from? I don’t see a LINE command in pymol/modules/cgo.py -David > On Dec 22, 2014, at 11:40 AM, Robert Hanson wrote: > > OK. I will look at the PyMOL code if I need to. For instance: > > LINE has eight parameters. I don't know what the firs

Re: [PyMOL] sulfated tyrosine's losing connection

use the CONECT records. -David > On Dec 23, 2014, at 12:20 AM, Jordan Willis wrote: > > Does anyone know why PyMoL renders the PDBs 3U2S and 3U4E without connecting > backbone atoms at residue 100G and 100H? Are the bond distances for these two > residue types not within the r

Re: [PyMOL] Scripting attempts

(a) I'll let someone else say whether you can use range in pml files, not completely sure on that one and the formatting rules. personally, I would write this in python, and you would need a : after the range (b) you are missing any indication of what %4d refers to. See example 3.23 on http://www.

Re: [PyMOL] MacPyMOL fink download

(2) assuming you didn't change it when installing fink, fink will install pymol in the /sw/bin directory. (4) this is fink setting environment variables such as PATH. You can add a line to your .bashrc to source it so it will be sourced every time you open a terminal. On Mon, Jan 19, 2015 at

Re: [PyMOL] Compilation problem with Pymol v1.7.4.0

roblem. > > Dwayne > > > layer3/Executive.cpp:13998: error: ‘glutLeaveFullScreen’ was not declared in > this scope This was fixed in the svn commit following 1.7.4.0 (commit 4105) http://sourceforge.net/p/pymol/code/4107/log/?path=/trunk <http://sour

Re: [PyMOL] The problem of save molecule to PDB after mutagenesis wizard

This occurs when retain_order is set before loading a protein. You have to: unset retain_order Then load your protein again. You might say: "I didn't set retain_order". This is likely true. Some very popular pymol plugins set it when loaded, most famously the autodock plugin.

Re: [PyMOL] Ball and stick model

http://pymolwiki.org/index.php/Ball_and_Stick ? You used the "handmade" method on that page. Generally, I like using the preset better. On Sun, Feb 1, 2015 at 11:42 PM, Seera Suryanarayana wrote: > Dear Pymol Users > I would like to represent the protein what I have in ball and stick model. > I

Re: [PyMOL] green rings

you can set cartoon_ring_color ? > 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 >

Re: [PyMOL] APBS plugin not working on both Ubuntu & Windows 7

of other things ./configure appears to do, I suggest following the steps in the INSTALL file. -David On Tue, Apr 14, 2015 at 2:39 AM, Brenton Horne wrote: > Hi, > > pdb2pqr.py doesn't exist in the pdb2pqr tar.gz file (for either 2.0.0 or > 1.8 versions; in a previous quest

Re: [PyMOL] PyMOL ball & stick representation of imatinib in 2HYY

preset.ball_and_stick('r. STI’) > On Apr 23, 2015, at 12:52 PM, Brenton Horne wrote: > > Hi, > > I recently read this reply > (http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg13248.html > ) > to

Re: [PyMOL] SCWRL version with educational-use PyMOL?

I believe all versions of Pymol use the 2002 version of the library. -David > On Jun 1, 2015, at 1:32 PM, Emilia C. Arturo (Emily) wrote: > > Hello. > > Does anyone know which version of SCWRL (backbone-dependent rotamer library) > is used in the educational-use-onl

Re: [PyMOL] opensource for commercial use?

ay for a couple hours of a lawyer's time to understand what you should do to comply with the license. -David On Fri, Jul 3, 2015 at 10:39 AM, Albert wrote: > Hello: > > I just got a question: can we use the open source version of pymol for > commercial usage? Or can we develop som

Re: [PyMOL] how can we rotate torsion angle of a molecule?

dex.php/Mutagenesis> (using without mutating gives you rotamers for a residue) http://www.pymolwiki.org/index.php/Rotamer_Toggle <http://www.pymolwiki.org/index.php/Rotamer_Toggle> -David-- Don't Limit Your

Re: [PyMOL] Problem with loadBfact.py on windows

This is the problem. Pymol’s working directory is not where you have this file. So, the script never loads. > On Jul 10, 2015, at 12:20 PM, ABEL Stephane 175950 > wrote: > > No such file or directory: './loadB2Fact.py'

Re: [PyMOL] How to find RMSD values using fitting.py using Shell script

http://www.pymolwiki.org/index.php/Command_Line_Options see the -c and -r options. I also use -q pymol -qcr script.py — arg1 arg2 arg3 > On Jul 10, 2015, at 8:44 AM, Gazal wrote: > > Hi, > > I'm trying to find the RMSD values for bat

Re: [PyMOL] How to find RMSD values using fitting.py using Shell script

??) I left in questions for the select1 and select2 arguments of the function since it is not at all clear what you would like to put in as arguments there. Beyond that, I would recommend reading up on python assuming you are not familiar with the language. -David > On Jul 11, 2015, at

Re: [PyMOL] Python from PyMOL or PyMOL from Python?

I vastly prefer calling the python program from pymol You can call any python program using pymol as: pymol -r program.py — arg1 arg2 arg3 Or, my full preferred method is: pymol -qrck program.py — arg1 arg2 arg3 These make it quieter, stay on the command line, and not read the .pymolrc file

Re: [PyMOL] creation of a sphere

What version of PyMol are you using? > On Aug 27, 2015, at 7:50 AM, Christian Trindler > wrote: > > Hello, > > I’ve been trying to make a pseudoatom/sphere simply by typing: > pseudoatom name > into the command line of Pymol, but it only gives me the following error > message instead of the

Re: [PyMOL] Using cartoon putty-like command

presumably: http://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/modules/pymol/preset.py#l164 On Mon, Oct 5, 2015 at 5:42 AM, Clavel wrote: > Hello everyone, > > I would like to create my own command within the pymol environement. > > I have currently a set of points in a pdb files with

Re: [PyMOL] pymol to webGL?

You can set: pse_export_version to the 3-part version of pymol you would like to use as an export version. -David > On Oct 18, 2015, at 3:48 AM, Takanori Nakane > wrote: > > Hi, > > It looks like the structure of PyMOL session (what > we got from cmd.get_session)

Re: [PyMOL] Pymol Morph movie error

me magical updated version floating around out there, but I doubt it. Otherwise, no new features in 20 years and no bug/compatibility fixes in 13. -David On Mon, Oct 19, 2015 at 8:36 AM, wrote: > Dear Pymol community, > > > > Im using Pymol 1.7.6 and created a morph mo

Re: [PyMOL] Pymol Morph movie error

/trunk/src/mpeg_encode/ -David > On Oct 20, 2015, at 4:46 AM, > wrote: > > Dear Thomas, David, > > I appreciate your help. > First I'm using windows 7. > > The link from: > http://freemol.org <http://freemol.org/> > leading to > http://bmrc.be

Re: [PyMOL] placing protein into lipid bilayer

I would disagree with your assertion that they use pymol to "insert" the protein into the membrane. They use the program they wrote, g_membed, to insert the protein. They used pymol to overlap them for the beginning of the simulation. That is, they use pymol to place the atoms of the protein on top

Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

Assuming you are ok with overwriting the B-factors stored.y=[] iterate_state 1, prot, stored.y.append(y) % prot here should be replaced with your pymol object name alter prot, b=stored.y.pop(0) % again, replace prot with your pymol object name On Wed, Nov 18, 2015 at 7:49 AM, Smith Liu wrote

Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

I forgot: spectrum b at the end. On Wed, Nov 18, 2015 at 8:11 AM, David Hall wrote: > Assuming you are ok with overwriting the B-factors > > > stored.y=[] > iterate_state 1, prot, stored.y.append(y) % prot here should be replaced > with your pymol object name > alter p

Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

9:12 AM, Smith Liu wrote: Dear David, I am unfamiliar with the pymol scripts so I do not understands where your scripts end at each line. Can we write this way, stored.y=[] iterate_state 1, prot, stored.y.append(y) alter prot, b=stored.y.pop(0) which means those from % in your scripts will be

Re: [PyMOL] on PDB

http://pymolwiki.org/index.php/Save ?? -David > On Nov 24, 2015, at 9:45 PM, Smith Liu wrote: > > Dear All, > > Suppose the original PDB was not oriented. Once we have it oriented by pymol, > is any way we can save the new PDB or

Re: [PyMOL] Pymol under El Capitan

Try the last comment on: https://github.com/Homebrew/homebrew-science/issues/2273 -David On Fri, Dec 11, 2015 at 3:39 AM, Chris Swain wrote: > Hi, > > I maintain a list of science applications that work under El Capitan ( > http://www.macinchem.org/blog/files/c92b0faf48c1bb7dee5e

Re: [PyMOL] Pymol issues for coloring ball and stick representation

set_bond stick_color, color, selection For more info on what is used to create the ball and stick preset, see: http://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/modules/pymol/preset.py#l144 -David > On Dec 17, 2015, at 2:35 AM, ANURAG SANKHYAN wrote: > > Dear all > &

Re: [PyMOL] optimize and open babel troubles

Ubuntu’s universe repository has a 32-bit version of pymol? http://packages.ubuntu.com/precise/pymol Obviously, being a 4-year old distro, it is an older release, but it may still work with the plugin. -David > On Jan 6, 2016, at 2:39 PM, Joe Gauthier wrote: > > Hello all, > &

Re: [PyMOL] pdb edition

mode http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol#move And then save http://pymolwiki.org/index.php/Save But honestly, the description sounds like something that would be infinitely easier to do using some plain python code rather than in pymol. -David > On Jan 19, 2016,

Re: [PyMOL] Filled rings on stick mode

would something like these work for you? fetch 1rna, async=0 as cartoon set cartoon_ring_mode, 1 cartoon skip show sticks set cartoon_ladder_mode, 0 > On Jan 28, 2016, at 6:28 PM, COSTA Maria > wrote: > > Hi, > > I would like to know if it is possible to have the rings filled for the > nucle

Re: [PyMOL] auto_show_cartoon or similar

My thoughts exactly! Dave Bourgaize On 2/8/16, 9:54 AM, "H. Adam Steinberg" wrote: >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 sticksŠ yikes! > >YES!!! to the default being secondary structure, ligands as sticks

Re: [PyMOL] why lib/python folder is missing?

Doesn’t using --install-lib mean you are explicitly telling it to put the files in your modules directory instead of creating any lib/python type directories? > On Mar 5, 2016, at 2:50 PM, Albert wrote: > > Hello: > > I am using the following command line to compile PYmol: > > setenv prefix

[PyMOL] .psw in Powerpoint for Mac

ate a hyperlink in powerpoint, powerpoint can't figure open the file... Where am I going wrong... I'm sure this is really simple.. But I can figure it out. Cheers, Dave -- *** Dr David Briggs| Structural

Re: [PyMOL] problem getting kabsch.py to run

Maggie, I found that I need to install the python-scientific package for my distro (Ubuntu Dapper) in order to get the LinearAlgebra and Matrix python modules required by the script. Can you forward the error message you're getting when you try to run kabsch.py in pymol? Best, David

[PyMOL] Anisotropic b-value thermal ellipsoids

Hi - I'd like to make some anisotropic b-value thermal ellipsoids using PyMol. I found one script at google, but can't get it to recognize the 5 programs I had to download to try to get it to run. Does anyone have an easy way to do this. I want to use the ANISOU terms genereated by shelxl. I'm u

[PyMOL] Projecting shadows onto a background.

Hi Pymol-ers. Does anyone know how I can use pymol to project a shadow of my protein onto a background? Cheers, Dave -- --- David Briggs, PhD. Father & Crystallographer www.dbriggs.talktalk.net iChat AIM ID: DBassophile

Re: [PyMOL] Morphing movie

__ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- --- David Briggs, PhD. Father & Crystallographer www.dbriggs.talktalk.net iChat AIM ID: DBassophile

[PyMOL] setting dash_lenth to another value for certain bonds

Hi - I have some hydrogen bonds and metal-ligand bonds that we want to look differently. On MacPymol I used: Wizard>>Measurement to create the bonds I can manipulate how the look under: Setting>>Edit All and changing parameters under the "Dash" settings. Is there some command line input I can

[PyMOL] question on "state"

This regards to my last post. I finally got it with: PyMOL>set dash_length, 0.1, measure01, 1 and got the message: Setting: dash_length set to 0.1 in object "measure01", state 1. but was wondering what "state" actually refers too... ie. previously, I tried: PyMOL>set "dash_length", 0.1, mea

[PyMOL] colour by rms...

Hi everyone... I'm sure this has been covered in the pymol mailing list previously, but I've looked back 12months and I can't find it. Can I colour a structure by its rmsd from another strucutre. Thanks in advance Dave -- --- David Brig

Re: [PyMOL] Has anybody successfully compiled pymol with MingW?

se ran without problems. It was the same version of Python on both platforms, but gcc 4.1.2 on Linux and 4.2.1-sjlj on Mingw. I suspect platform specific changes in types, as caught by the various warning messages noted above. Anybody know a way to force pymol to run in a mode that will give some hint as to where this is going wrong? How does one start pymol up within Idle? Thanks, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech

[PyMOL] Building pymol on Windows?

successfully built PyMol on Windows? If so, please let us know how it was done. Thanks, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech

Re: [PyMOL] Has anybody successfully compiled pymol with MingW?

on. The latter is a lot bigger though, at 11.1Mb whereas the former is only 2.0 Mb. I tried copying _cmd.pyd to the python DLLs directory, but that didn't help. Any ideas? So close, and yet, so far... Thanks, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech

[PyMOL] Problems importing pymol functionality under a python script.

File "pymol.py", line 4, in ? pymol.finish_launching() AttributeError: 'module' object has no attribute 'finish_launching' Does anybody know what's going on ? Thanks in advance David McGiven

Re: [PyMOL] Problems importing pymol functionality under a pythonscript.

; object has no attribute 'finish_launching' >>> from pymol import cmd Traceback (most recent call last): File "", line 1, in ? ImportError: cannot import name cmd >>> Does anybody else know what might be the problem ? Thanks in advance David On Thu, 4

[PyMOL] Using a .png/.tif file as a cgo_plane type object.

Hi everyone. Is there a way in pymol to use a .png or a .tif as a cgo_plane type object, to place behind a structure (and optionally cast shadows across)? Cheers, David -- David C. Briggs PhD Father & Crystallographer http://personalpages.manchester.ac.uk/s

[PyMOL] How to move aligned objects apart

I have three molecules aligned on each other. I would like to move them apart so that I can make a .png file with all three of them aligned, but simply translated apart. I have tried the translate [x, x, x] command but no success. Advice? thanks, Dave --

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