pymol-users Mailing List for PyMOL Molecular Graphics System

Hello, I would like to merge two PyMOL session. I found the suggestion 
below, but would appreciate some details on how to use this. Thanks, Mike
you could use the following function to write out a script which recreates all current selections.
from pymol import cmd
@cmd.extend
def dump_selections(filename):
 '''
DESCRIPTION
 Dump a script which recreates all current named selections
 '''
 handle = open(filename, 'w')
 for name in cmd.get_names('selections'):
 for (model, index) in cmd.index(name):
 print >> handle, 'cmd.select("%s", "(%s`%d)", merge=1)' % (
 name, model, index)
Hope that helps.
Cheers,
 Thomas

Ah, I see. I just use files that others send me. Yes, this was from
MacPyMOL. The "main" dictionary item does seem supremely useful. Is there a
way of deriving that information from the PSE file? Otherwise, how does one
reproduce an image created by PyMOL from a session file?
On Wed, Dec 23, 2015 at 8:53 PM, Thomas Holder <
tho...@sc...> wrote:
> Hi Bob,
>
> Nothing has changed here in 1.8. I assume you used MacPyMOL recently? As
> far as I know, MacPyMOL never stored the "main" dictionary item. Or if you
> export a session with partial=1, it will also not store the viewport.
>
> Cheers,
> Thomas
>
> On 23 Dec 2015, at 19:12, Robert Hanson <ha...@st...> wrote:
>
> > I have a question about the PSE file format.
> >
> > Newer PSE files, perhaps those created using PyMOL 1.8, seem to have no
> indication of the desired viewport width and height. These were in the
> "main" dictionary item. Is there any way in these new files to find out the
> original viewport size?
> >
> > Bob
> >
> > --
> > Robert M. Hanson
> > Larson-Anderson Professor of Chemistry
> > Chair, Department of Chemistry
> > St. Olaf College
> > Northfield, MN
> > http://www.stolaf.edu/people/hansonr
> >
> > If nature does not answer first what we want,
> > it is better to take what answer we get.
> >
> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

Hi Bob,
Nothing has changed here in 1.8. I assume you used MacPyMOL recently? As far as I know, MacPyMOL never stored the "main" dictionary item. Or if you export a session with partial=1, it will also not store the viewport.
Cheers,
 Thomas
On 23 Dec 2015, at 19:12, Robert Hanson <ha...@st...> wrote:
> I have a question about the PSE file format. 
> 
> Newer PSE files, perhaps those created using PyMOL 1.8, seem to have no indication of the desired viewport width and height. These were in the "main" dictionary item. Is there any way in these new files to find out the original viewport size? 
> 
> Bob
> 
> -- 
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
> 
> If nature does not answer first what we want,
> it is better to take what answer we get. 
> 
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

I have a question about the PSE file format.
Newer PSE files, perhaps those created using PyMOL 1.8, seem to have no
indication of the desired viewport width and height. These were in the
"main" dictionary item. Is there any way in these new files to find out the
original viewport size?
Bob
-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

?Hi Anurag,
Try:
set_bond stick_color, color, selection
Where color is your color of choice and selection is the object for which you want to change the bond color.
Best wishes,
 Jim
________________________________
From: ANURAG SANKHYAN <an...@th...>
Sent: Thursday, December 17, 2015 2:35 PM
To: pym...@li...
Subject: [PyMOL] Pymol issues for coloring ball and stick representation
Dear all
I am a user of PyMol using an academic version (free).
I am trying to develop a 3D model for my protein-protein interactions. I have chosen a ball and stick preset representations.
The problem is that I cannot get a single color for the stick and the ball for representing my molecule. While the ball color is easily changed, the stick color remains grey. I have tried most of the options for color change but am not getting the desired results. Any suggestions for this?
Anurag

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 <an...@th...> wrote:
> 
> Dear all
> 
> I am a user of PyMol using an academic version (free). 
> I am trying to develop a 3D model for my protein-protein interactions. I have chosen a ball and stick preset representations.
> The problem is that I cannot get a single color for the stick and the ball for representing my molecule. While the ball color is easily changed, the stick color remains grey. I have tried most of the options for color change but am not getting the desired results. Any suggestions for this?
> 
> Anurag
> ------------------------------------------------------------------------------
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Dear all
I am a user of PyMol using an academic version (free).
I am trying to develop a 3D model for my protein-protein interactions. I
have chosen a ball and stick preset representations.
The problem is that I cannot get a single color for the stick and the ball
for representing my molecule. While the ball color is easily changed, the
stick color remains grey. I have tried most of the options for color change
but am not getting the desired results. Any suggestions for this?
Anurag

Don't worry. No apology necessary. It's a closely held secret that JSmol
can do this. In any case, trust me, you will find plenty that JSmol cannot
handle. There are many mysteries of the PSE format that I could only guess
at.
Enjoy!
​

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 <ha...@st...> 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
Lodi, WI 53555
608/592-2366

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
I certainly don't claim to know anything about JyMOL, except I guess it
uses JNLP. Does Chrome support JNLP anymore?
Bob Hanson

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
Lodi, WI 53555
608/592-2366

Greetings PyMOL users,
Please join me in congratulating Dr. Julian Heinrich, who has been awarded the Warren L. DeLano Memorial PyMOL Open Source Fellowship for 2015–2016.
Julian will work on automated view selection for molecular structures. Setting up a view (camera orientation) which maximizes the visibility of relevant features is critical when creating figures and movies. An automated view selection will improve the output of automated figure generation pipelines, it can assist the user when manually searching for the best view, and it can be used to generate automatic tour movies with the N best views. Julian will also help maintaining the PyMOLWiki and pymol-users mailing list. You can reach Julian at ju...@jo....
The Warren L. DeLano Memorial PyMOL Open-Source Fellowship is awarded
by Schrӧdinger to supplement the income of an outstanding member of
the PyMOL open-source community so that s/he can continue to develop
free resources to help scientific progress and the community as a
whole. You can read more about the PyMOL Open Source Fellowship
Program and the fellows at http://pymol.org/fellowship.
Cheers,
 Thomas & the PyMOL Team at Schrödinger
-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Damien,
The following code bins particles and makes a grid of pseudoatoms, putting
the count in the b-factor field and as radius. You should be able to
convert these to cubes using the script (but doing scaled spheres, and
coloring according to count is nifty too).
import numpy
def griddify(selection='all', bins=24, name="grrrrid"):
 """Count particles in grid cells and generate pseudatoms for cell
centers"""
 X=numpy.array(cmd.get_model().get_coord_list())
 lo = X.min()
 up = X.max()
 rng = up-lo
 bins2 = bins*bins
 Y = ((bins-1e-8)*(X-lo)/rng).astype('int')
 Y[:,1] *= bins
 Y[:,2] *= bins2
 B = numpy.bincount( Y.sum(axis=1) )
 for a,b in enumerate(B):
 if b:
 x = l + rng*(a%bins+0.5)/bins
 y = l + rng*((a%(bins2))/bins+0.5)/bins
 z = l + rng*(a/(bins2)+0.5)/bins
 cmd.pseudoatom(name,pos=(x,y,z), b=b,vdw=b)
Hope it helps,
Tsjerk
On Fri, Dec 11, 2015 at 6:50 PM, Damien Clavel <dc...@ib...> wrote:
> Hi Tsjerk,
>
> As a matter of fact the replacement of atoms by cubes is possible with
> cubes.py. However, this applet doesn't suit my project.
> Indeed, I would like to get a script that describe your second guess!
>
> D
> Le 11/12/15 17:12, Tsjerk Wassenaar a écrit :
>
>
> Hi Damien,
>
> Do you mean replacing the atoms by cubes, or by binning the atoms on a 3D
> grid and show these cubes if filled?
>
> Cheers,
>
> Tsjerk
>
> On Fri, Dec 11, 2015 at 4:51 PM, Damien Clavel <dc...@ib...> wrote:
>
>> Good evening pymol users,
>>
>> I would like to represent a protein with a superimposed 3D grid of cubes.
>> I tried the applet cubes.py but it is not appropriate for me...
>>
>> So my goal is to control the size of the cubes that will be part of such
>> grid.
>> In addition, it will be really great if I could even control the color
>> (shaded) of each cubes.
>>
>> Does anyone could help me?
>>
>> --
>> *Damien CLAVEL*
>> Cellphone +33 7 81 66 61 70
>> Landline +33 4 57 42 87 35
>> PhD student at Laboratoire Chimie Physique (UP Sud)
>> and Institut de Biologie Structurale (EPN Campus)
>> --------------------------------------------------------------------------
>> Laboratoire de Chimie Physique
>> <http://www.lcp.u-psud.fr/rubrique.php3?id_rubrique=266/> Institut de
>> Biologie Structurale <http://www.ibs.fr/spip.php?lang=en>
>> Bul. 350 Campus Orsay EPN Campus
>> 15, Av. Jean Perrin 6, rue Jules Horowitz
>> F-91405 ORSAY Cedex F-38000 GRENOBLE
>>
>> [image: Image and video hosting by TinyPic]
>> <http://tinypic.com?ref=28s7yvd>
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
> --
> *Damien CLAVEL*
> Cellphone +33 7 81 66 61 70
> Landline +33 4 57 42 87 35
> PhD student at Laboratoire Chimie Physique (UP Sud)
> and Institut de Biologie Structurale (EPN Campus)
> --------------------------------------------------------------------------
> Laboratoire de Chimie Physique
> <http://www.lcp.u-psud.fr/rubrique.php3?id_rubrique=266/> Institut de
> Biologie Structurale <http://www.ibs.fr/spip.php?lang=en>
> Bul. 350 Campus Orsay EPN Campus
> 15, Av. Jean Perrin 6, rue Jules Horowitz
> F-91405 ORSAY Cedex F-38000 GRENOBLE
>
> [image: Image and video hosting by TinyPic]
> <http://tinypic.com?ref=28s7yvd>
>
-- 
Tsjerk A. Wassenaar, Ph.D.

Dear:
I've compiled pymol-1.8.0 under my Linux X64 OS. I found that Pymol can 
start by command:
pymol
without any complaints or erros. However, when I try to load a .pdb file 
into pymol, pymol always failed with following messages:
-----------------------------------------------------------------------------------------------
stephen@linux:~/tmp> pymol 4eiy.pdb
 PyMOL(TM) Molecular Graphics System, Version 1.8.0.0.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.
 Created by Warren L. DeLano, Ph.D.
 PyMOL is user-supported open-source software. Although some versions
 are freely available, PyMOL is not in the public domain.
 If PyMOL is helpful in your work or study, then please volunteer
 support for our ongoing efforts to create open and affordable 
scientific
 software by purchasing a PyMOL Maintenance and/or Support subscription.
 More information can be found at "http://www.pymol.org".
 Enter "help" for a list of commands.
 Enter "help <command-name>" for information on a specific command.
 Hit ESC anytime to toggle between text and graphics.
 Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 1.30.
 OpenGL graphics engine:
 GL_VENDOR: VMware, Inc.
 GL_RENDERER: Gallium 0.4 on llvmpipe (LLVM 3.4, 256 bits)
 GL_VERSION: 2.1 Mesa 10.0.3
 Detected 4 CPU cores. Enabled multithreaded rendering.
HEADER MEMBRANE PROTEIN 06-APR-12 4EIY
TITLE CRYSTAL STRUCTURE OF THE CHIMERIC PROTEIN OF A2AAR-BRIL IN COMPLEX
TITLE 2 WITH ZM241385 AT 1.8A RESOLUTION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ADENOSINE RECEPTOR A2A/SOLUBLE CYTOCHROME B562 CHIMERA;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: CYTOCHROME B-562;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 CmdLoad: "4eiy.pdb" loaded as "4eiy".
/home/stephen/install/pymol-1.8.0/pymol: line 3: 10490 Segmentation 
fault "/usr/bin/python" 
"/home/stephen/install/pymol-1.8.0/modules/pymol/__init__.py" "$@"
-----------------------------------------------------------------------------
I am just wondering what's the problem? I also tried .cif, .mol2 files, 
and all of them failed.
thx a lot

Hi Tsjerk,
As a matter of fact the replacement of atoms by cubes is possible with 
cubes.py. However, this applet doesn't suit my project.
Indeed, I would like to get a script that describe your second guess!
D
Le 11/12/15 17:12, Tsjerk Wassenaar a écrit :
>
> Hi Damien,
>
> Do you mean replacing the atoms by cubes, or by binning the atoms on a 
> 3D grid and show these cubes if filled?
>
> Cheers,
>
> Tsjerk
>
> On Fri, Dec 11, 2015 at 4:51 PM, Damien Clavel <dc...@ib... 
> <mailto:dc...@ib...>> wrote:
>
> Good evening pymol users,
>
> I would like to represent a protein with a superimposed 3D grid of
> cubes.
> I tried the applet cubes.py but it is not appropriate for me...
>
> So my goal is to control the size of the cubes that will be part
> of such grid.
> In addition, it will be really great if I could even control the
> color (shaded) of each cubes.
>
> Does anyone could help me?
>
> -- 
> *Damien CLAVEL*
> Cellphone +33 7 81 66 61 70 <tel:%2B33%207%2081%2066%2061%2070>
> Landline +33 4 57 42 87 35 <tel:%2B33%204%2057%2042%2087%2035>
> PhD student at Laboratoire Chimie Physique (UP Sud)
> and Institut de Biologie Structurale (EPN Campus)
> --------------------------------------------------------------------------
> Laboratoire de Chimie Physique
> <http://www.lcp.u-psud.fr/rubrique.php3?id_rubrique=266/> Institut
> de Biologie Structurale <http://www.ibs.fr/spip.php?lang=en>
> Bul. 350 Campus Orsay EPN Campus
> 15, Av. Jean Perrin 6, rue Jules Horowitz
> F-91405 ORSAY Cedex F-38000 GRENOBLE
>
> Image and video hosting by TinyPic <http://tinypic.com?ref=28s7yvd>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...
> <mailto:PyM...@li...>)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives:
> http://www.mail-archive.com/pym...@li...
>
>
>
>
> -- 
> Tsjerk A. Wassenaar, Ph.D.
>
-- 
*Damien CLAVEL*
Cellphone +33 7 81 66 61 70
Landline +33 4 57 42 87 35
PhD student at Laboratoire Chimie Physique (UP Sud)
 and Institut de Biologie Structurale (EPN Campus)
--------------------------------------------------------------------------
Laboratoire de Chimie Physique 
<http://www.lcp.u-psud.fr/rubrique.php3?id_rubrique=266/> Institut de 
Biologie Structurale <http://www.ibs.fr/spip.php?lang=en>
 Bul. 350 Campus Orsay EPN Campus
 15, Av. Jean Perrin 6, rue Jules Horowitz
 F-91405 ORSAY Cedex F-38000 GRENOBLE
Image and video hosting by TinyPic <http://tinypic.com?ref=28s7yvd>

Hi Damien,
Do you mean replacing the atoms by cubes, or by binning the atoms on a 3D
grid and show these cubes if filled?
Cheers,
Tsjerk
On Fri, Dec 11, 2015 at 4:51 PM, Damien Clavel <dc...@ib...> wrote:
> Good evening pymol users,
>
> I would like to represent a protein with a superimposed 3D grid of cubes.
> I tried the applet cubes.py but it is not appropriate for me...
>
> So my goal is to control the size of the cubes that will be part of such
> grid.
> In addition, it will be really great if I could even control the color
> (shaded) of each cubes.
>
> Does anyone could help me?
>
> --
> *Damien CLAVEL*
> Cellphone +33 7 81 66 61 70
> Landline +33 4 57 42 87 35
> PhD student at Laboratoire Chimie Physique (UP Sud)
> and Institut de Biologie Structurale (EPN Campus)
> --------------------------------------------------------------------------
> Laboratoire de Chimie Physique
> <http://www.lcp.u-psud.fr/rubrique.php3?id_rubrique=266/> Institut de
> Biologie Structurale <http://www.ibs.fr/spip.php?lang=en>
> Bul. 350 Campus Orsay EPN Campus
> 15, Av. Jean Perrin 6, rue Jules Horowitz
> F-91405 ORSAY Cedex F-38000 GRENOBLE
>
> [image: Image and video hosting by TinyPic]
> <http://tinypic.com?ref=28s7yvd>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
-- 
Tsjerk A. Wassenaar, Ph.D.

Good evening pymol users,
I would like to represent a protein with a superimposed 3D grid of cubes.
I tried the applet cubes.py but it is not appropriate for me...
So my goal is to control the size of the cubes that will be part of such 
grid.
In addition, it will be really great if I could even control the color 
(shaded) of each cubes.
Does anyone could help me?
-- 
*Damien CLAVEL*
Cellphone +33 7 81 66 61 70
Landline +33 4 57 42 87 35
PhD student at Laboratoire Chimie Physique (UP Sud)
 and Institut de Biologie Structurale (EPN Campus)
--------------------------------------------------------------------------
Laboratoire de Chimie Physique 
<http://www.lcp.u-psud.fr/rubrique.php3?id_rubrique=266/> Institut de 
Biologie Structurale <http://www.ibs.fr/spip.php?lang=en>
 Bul. 350 Campus Orsay EPN Campus
 15, Av. Jean Perrin 6, rue Jules Horowitz
 F-91405 ORSAY Cedex F-38000 GRENOBLE
Image and video hosting by TinyPic <http://tinypic.com?ref=28s7yvd>

That seems to have sorted things.
Many Thanks
Chris
> On 11 Dec 2015, at 13:14, David Hall <li...@co...> wrote:
> 
> Try the last comment on:
> 
> https://github.com/Homebrew/homebrew-science/issues/2273 <https://github.com/Homebrew/homebrew-science/issues/2273>
> 
> -David
> 
> On Fri, Dec 11, 2015 at 3:39 AM, Chris Swain <sw...@ma... <mailto:sw...@ma...>> wrote:
> Hi,
> 
> I maintain a list of science applications that work under El Capitan (http://www.macinchem.org/blog/files/c92b0faf48c1bb7dee5eeba1260cff43-1657.php <http://www.macinchem.org/blog/files/c92b0faf48c1bb7dee5eeba1260cff43-1657.php>) and I tried a pre installed version of Pymol and it worked without issue. However I have had a few readers email me saying they are having problems so I took a new machine running El Capitan and tried to instal a variety of cheminformatics tools including Pymol using Homebrew and PIP as described here (http://www.macinchem.org/reviews/cheminfo/cheminfoMac.php <http://www.macinchem.org/reviews/cheminfo/cheminfoMac.php>). All worked fine except Pymol which opened but crashed with the following error.
> 
> Username:~ prompt$ pymol
> PyMOL(TM) Molecular Graphics System, Version 1.7.6.0.
> Copyright (c) Schrodinger, LLC.
> All Rights Reserved.
> 
> Created by Warren L. DeLano, Ph.D. 
> 
> PyMOL is user-supported open-source software. Although some versions
> are freely available, PyMOL is not in the public domain.
> 
> If PyMOL is helpful in your work or study, then please volunteer 
> support for our ongoing efforts to create open and affordable scientific
> software by purchasing a PyMOL Maintenance and/or Support subscription.
> 
> More information can be found at "http://www.pymol.org <http://www.pymol.org/>".
> 
> Enter "help" for a list of commands.
> Enter "help <command-name>" for information on a specific command.
> 
> Hit ESC anytime to toggle between text and graphics.
> 
> Detected OpenGL version 2.0 or greater. Shaders available.
> Detected GLSL version 1.20.
> OpenGL graphics engine:
> GL_VENDOR: NVIDIA Corporation
> GL_RENDERER: NVIDIA GeForce 8600M GT OpenGL Engine
> GL_VERSION: 2.1 NVIDIA-10.0.40 310.90.10.05b12
> Detected 2 CPU cores. Enabled multithreaded rendering.
> libpng warning: Application built with libpng-1.6.19 but running with 1.5.23
> /usr/local/bin/pymol: line 4: 3628 Segmentation fault: 11 "/usr/local/opt/python/bin/python2.7" "/usr/local/Cellar/pymol/1.7.6.0/libexec/lib/python2.7/site-packages/pymol/__init__.py <http://1.7.6.0/libexec/lib/python2.7/site-packages/pymol/__init__.py>" "$@"
> 
> Any suggestions?
> 
> Cheers
> Chris
> 
> ------------------------------------------------------------------------------
> 
> _______________________________________________
> PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...>)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users <https://lists.sourceforge.net/lists/listinfo/pymol-users>
> Archives: http://www.mail-archive.com/pym...@li... <http://www.mail-archive.com/pym...@li...>
> 

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 <sw...@ma...> wrote:
> Hi,
>
> I maintain a list of science applications that work under El Capitan (
> http://www.macinchem.org/blog/files/c92b0faf48c1bb7dee5eeba1260cff43-1657.php)
> and I tried a pre installed version of Pymol and it worked without issue.
> However I have had a few readers email me saying they are having problems
> so I took a new machine running El Capitan and tried to instal a variety of
> cheminformatics tools including Pymol using Homebrew and PIP as described
> here (http://www.macinchem.org/reviews/cheminfo/cheminfoMac.php). All
> worked fine except Pymol which opened but crashed with the following error.
>
> Username:~ prompt$ pymol
> PyMOL(TM) Molecular Graphics System, Version 1.7.6.0.
> Copyright (c) Schrodinger, LLC.
> All Rights Reserved.
>
>
> Created by Warren L. DeLano, Ph.D.
>
>
> PyMOL is user-supported open-source software. Although some versions
> are freely available, PyMOL is not in the public domain.
>
>
> If PyMOL is helpful in your work or study, then please volunteer
> support for our ongoing efforts to create open and affordable
> scientific
> software by purchasing a PyMOL Maintenance and/or Support subscription.
>
> More information can be found at "http://www.pymol.org".
>
>
> Enter "help" for a list of commands.
> Enter "help <command-name>" for information on a specific command.
>
> Hit ESC anytime to toggle between text and graphics.
>
> Detected OpenGL version 2.0 or greater. Shaders available.
> Detected GLSL version 1.20.
> OpenGL graphics engine:
> GL_VENDOR: NVIDIA Corporation
> GL_RENDERER: NVIDIA GeForce 8600M GT OpenGL Engine
> GL_VERSION: 2.1 NVIDIA-10.0.40 310.90.10.05b12
> Detected 2 CPU cores. Enabled multithreaded rendering.
> libpng warning: Application built with libpng-1.6.19 but running with
> 1.5.23
> /usr/local/bin/pymol: line 4: 3628 Segmentation fault: 11
> "/usr/local/opt/python/bin/python2.7" "/usr/local/Cellar/pymol/
> 1.7.6.0/libexec/lib/python2.7/site-packages/pymol/__init__.py" "$@"
>
> Any suggestions?
>
> Cheers
> Chris
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi,
I maintain a list of science applications that work under El Capitan (http://www.macinchem.org/blog/files/c92b0faf48c1bb7dee5eeba1260cff43-1657.php) and I tried a pre installed version of Pymol and it worked without issue. However I have had a few readers email me saying they are having problems so I took a new machine running El Capitan and tried to instal a variety of cheminformatics tools including Pymol using Homebrew and PIP as described here (http://www.macinchem.org/reviews/cheminfo/cheminfoMac.php). All worked fine except Pymol which opened but crashed with the following error.
Username:~ prompt$ pymol
 PyMOL(TM) Molecular Graphics System, Version 1.7.6.0.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.
 
 Created by Warren L. DeLano, Ph.D. 
 
 PyMOL is user-supported open-source software. Although some versions
 are freely available, PyMOL is not in the public domain.
 
 If PyMOL is helpful in your work or study, then please volunteer 
 support for our ongoing efforts to create open and affordable scientific
 software by purchasing a PyMOL Maintenance and/or Support subscription.
 More information can be found at "http://www.pymol.org".
 
 Enter "help" for a list of commands.
 Enter "help <command-name>" for information on a specific command.
 Hit ESC anytime to toggle between text and graphics.
 Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 1.20.
 OpenGL graphics engine:
 GL_VENDOR: NVIDIA Corporation
 GL_RENDERER: NVIDIA GeForce 8600M GT OpenGL Engine
 GL_VERSION: 2.1 NVIDIA-10.0.40 310.90.10.05b12
 Detected 2 CPU cores. Enabled multithreaded rendering.
libpng warning: Application built with libpng-1.6.19 but running with 1.5.23
/usr/local/bin/pymol: line 4: 3628 Segmentation fault: 11 "/usr/local/opt/python/bin/python2.7" "/usr/local/Cellar/pymol/1.7.6.0/libexec/lib/python2.7/site-packages/pymol/__init__.py" "$@"
Any suggestions?
Cheers
Chris

> On Fri, Dec 11, 2015 at 8:19 AM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
> 
>> Dear All,
>> 
>> Suppose by pymol I have opened A.pdb abd B.pdb. Is anyway I close B.pdb
>> and have only A.pdb displayed?
>> 
>> Smith
>> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Date: 2015年12月11日 08:53:37 +0100
> 
> just click the b.pdb on the Pymol object manager bar to undisplay it.
> 
> That's the basic of basic usage of Pymol. Wouldn't it be nice if you 
> spend a few minutes to go through Pymol manual?
> 
In a script, you do the same by specifying
disable(object)
enable (object)
Annemarie

just click the b.pdb on the Pymol object manager bar to undisplay it.
That's the basic of basic usage of Pymol. Wouldn't it be nice if you 
spend a few minutes to go through Pymol manual?
On 12/11/2015 08:19 AM, Smith Liu wrote:
> Dear All,
>
> Suppose by pymol I have opened A.pdb abd B.pdb. Is anyway I close 
> B.pdb and have only A.pdb displayed?
>
> Smith
>

Hi Smith,
You can delete the object:
delete B
Cheers,
Tsjerk
On Fri, Dec 11, 2015 at 8:19 AM, Smith Liu <smi...@16...> wrote:
> Dear All,
>
> Suppose by pymol I have opened A.pdb abd B.pdb. Is anyway I close B.pdb
> and have only A.pdb displayed?
>
> Smith
>
>
>
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
-- 
Tsjerk A. Wassenaar, Ph.D.

Dear All,
Suppose by pymol I have opened A.pdb abd B.pdb. Is anyway I close B.pdb and have only A.pdb displayed?
Smith

Dear all:
It appears that pymol only interpolates motions that include rotations by
moving the object along an arc. I would like to make a movie that does not
do this, but rather, moves the object along a straight line while rotating
the object. Unfortunately, I'm absolutely at a loss about how I could do
this. Would anybody have any suggestions about where to look for this
information?
Thanks,
Dan