date:20140609

Re: [PyMOL] command question RE printing out distances to text file

2014-06-09 Thread Lapolla, Suzanne M (HSC)

Thank you Robert and Thomas--I will try both and see what works best for my 
needs. 

From: Robert Campbell [robert.campb...@queensu.ca]
Sent: Monday, June 09, 2014 10:04 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] command question RE printing out distances to text file

Hi Suzanne,

You can also get the distance printed in the external GUI or terminal window
by using the "cmd.distance" version of the command.  So either you can
assign the distance to a variable and print it or you can print the result
directly.

Assuming you have two selections, sele1 and sele2 specifying the atoms of
interest you can do:

  d = cmd.distance(sele1,sele2)
  print sele1,sele2,d


Cheers,
Rob

On Mon, 2014-06-09
13:13 EDT, Thomas Holder  wrote:

> Hi Suzanne,
>
> you can use the get_distance command. It doesn't generate a distance
> object but prints the distance to the external window.
>
> https://urldefense.proofpoint.com/v1/url?u=http://pymolwiki.org/index.php/Get_Distance&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=921f4dfed39cd38f4ae7a70dfb937844d4e3faf1bc967c2f4d1f2944fa2ea31b
>
> Cheers,
>   Thomas
>
> On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC)
>  wrote:
>
> > Fellow Pymol Users:
> > I may have asked this question before...but if so have forgotten. I am
> > measuring distances between 2 atoms in 2 different objects using the
> > distance command, and it is working perfectly, but I wonder if there is
> > a command I can use/add so that those distances can be printed in the
> > external gui as well as being shown in the viewer. I will be doing lots
> > of these at the same time and the screen will get crowded. Thank you in
> > advance.
>




--
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

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Re: [PyMOL] Visualize Sheets from C-alpha Only Structure

2014-06-09 Thread Sean Law

Hi Darrell,
Thanks for the suggestion.
To make a long story short, we're publishing a new a method to assign secondary 
structure elements (SSE) solely from the C-alpha atoms (with ~95% accuracy 
relative to DSSP). We've compared this to backbone reconstruction schemes and 
the time to rebuild the backbone atoms is simply too time consuming (about an 
order of magnitude). In fact, the BBQ method claims to be "fast" but, based on 
my estimates, it's actually about twice as slow as the optimized "rebuild" 
program (when optimized to only rebuild the backbone atoms using basic 
geometry) from the MMTSB Tool Set by Michael Feig et al. Anyhow, my 
collaborator wanted to write a PyMOL plugin which will assign the SSEs using 
our program (for each state) and then display them nicely in PyMOL. This 
doesn't seem to be possible in PyMOL without reconstructing the backbone atoms. 
Yes, we can color each SSE accordingly but I was hoping that there was a better 
solution.
Best,
Sean

> From: darre...@niaid.nih.gov
> To: magic...@hotmail.com; jared.samp...@nyumc.org
> CC: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Visualize Sheets from C-alpha Only Structure
> Date: Wed, 4 Jun 2014 21:18:27 +
> 
> Hi Sean,
> 
> If you're doing this for illustrative purposes, why not just build the 
> inferred backbone? You could use BBQ, among many others:
> 
> http://biocomp.chem.uw.edu.pl/tools/bbq
> 
> FWIW,
> Darrell
> 
> --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
> 
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
> Office: 301-402-0095
> Mobile: 301-758-3559
> Web: BCBB Home 
> Page
> Twitter: @niaidbioit
> 
> Disclaimer: The information in this e-mail and any of its attachments is 
> confidential and may contain sensitive information. It should not be used by 
> anyone who is not the original intended recipient. If you have received this 
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> Diseases shall not accept liability for any statements made that are sender's 
> own and not expressly made on behalf of the NIAID by one of its 
> representatives.
> 
> From: Sean Law mailto:magic...@hotmail.com>>
> Date: Wednesday, June 4, 2014 4:17 PM
> To: "Sampson, Jared" mailto:jared.samp...@nyumc.org>>
> Cc: 
> "pymol-users@lists.sourceforge.net" 
> mailto:pymol-users@lists.sourceforge.net>>
> Subject: Re: [PyMOL] Visualize Sheets from C-alpha Only Structure
> 
> Jared,
> 
> For now, we are using different colors to indicate the SS assignments but 
> it's not pretty. We would prefer to show the SS for both sheets and helices.
> 
> Can you elaborate on what you mean by "radially symmetric". Are there other 
> cartoon modes where I would be able to get both helices and sheets after 
> altering the residue's SS assignment by hand? I see what you mean by not 
> being able to define the flat plane though.
> 
> Best,
> 
> Sean
> 
> 
> From: jared.samp...@nyumc.org
> To: magic...@hotmail.com
> CC: 
> pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Visualize Sheets from C-alpha Only Structure
> Date: Wed, 4 Jun 2014 20:03:54 +
> 
> Hi Sean -
> 
> I can confirm this behavior, but I’m not sure it’s unintentional on PyMOL’s 
> part.  Rather, I think it may have something to do with two facts: 1) unlike 
> loops, sheets represented in automatic mode are not radially symmetric; and 
> 2) unlike helices, the orientation of the sheet at a particular CA atom 
> cannot be determined by its immediate neighbors.  I haven’t had a chance to 
> look at the relevant source, so I can’t confirm this at the moment, but it 
> seems likely to me that PyMOL uses the other (non-CA) backbone atoms to 
> define the “flat” plane of a sheet, and without this information, instead of 
> guessing at its orientation, it omits the sheet entirely.  (This also appears 
> to be the case for other non-radially symmetric modes, including dumbbell, 
> rectangle, and oval.)
> 
> Could you get by using different colors to indicate your SS assignments in 
> another cartoon mode?
> 
> Cheers,
> Jared
> 
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/
> 
> 
> 
> 
> 
> 
> On Jun 4, 2014, at 1:50 PM, Sean Law 
> mailto:magic...@hotmail.com>> wrote:
> 
> Hi PyMOLers,
> 
> I have a c-alpha only model and I would like to visualize both helices and 
> sheets based on my own custom SS assignments (via "alter"). Altering a 
> residue's SS assignment to helix or loop (ss="H" or ss="L") is

[PyMOL] Pymol startup error

2014-06-09 Thread KK R

Hi,

I am suffering from pymol startup error. It gets terminated with the
following error messages:

 PyMOL(TM) Molecular Graphics System, Version 1.5.0.3.
 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 " for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 Detected OpenGL version 2.0 or greater. Shaders available.
*** buffer overflow detected ***: /usr/bin/python terminated
=== Backtrace: =
/lib64/libc.so.6(__fortify_fail+0x37)[0x7f30e5ee8277]
/lib64/libc.so.6(+0xfc350)[0x7f30e5ee6350]
/lib64/libc.so.6(+0xfb7d9)[0x7f30e5ee57d9]
/lib64/libc.so.6(_IO_default_xsputn+0x89)[0x7f30e5e623d9]
/lib64/libc.so.6(_IO_vfprintf+0x48a3)[0x7f30e5e35473]
/lib64/libc.so.6(__vsprintf_chk+0x97)[0x7f30e5ee5877]
/lib64/libc.so.6(__sprintf_chk+0x7d)[0x7f30e5ee57bd]
/usr/lib64/python2.7/site-packages/pymol/_cmd.so(CShaderMgr_ReadShaderFromDisk+0x2f3)[0x7f30e46ca8d3]
/usr/lib64/python2.7/site-packages/pymol/_cmd.so(CShaderPrg_NewFromFile+0x2e)[0x7f30e46cb71e]
/usr/lib64/python2.7/site-packages/pymol/_cmd.so(ShaderMgrConfig+0xa9)[0x7f30e46cb849]
/usr/lib64/python2.7/site-packages/pymol/_cmd.so(was_main+0x13e)[0x7f30e49bb8ce]
/usr/lib64/python2.7/site-packages/pymol/_cmd.so(+0x34b5c1)[0x7f30e497e5c1]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x113a)[0x7f30e646611a]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x143)[0x7f30e646b303]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0xd27)[0x7f30e6465d07]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x403)[0x7f30e646b5c3]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x7f30e64998b2]
/usr/lib64/libpython2.7.so.1.0(+0xf3d91)[0x7f30e64a6d91]
/usr/lib64/libpython2.7.so.1.0(PyRun_FileExFlags+0x86)[0x7f30e64a7156]
/usr/lib64/libpython2.7.so.1.0(PyRun_SimpleFileExFlags+0x17d)[0x7f30e64a7a2d]
/usr/lib64/libpython2.7.so.1.0(Py_Main+0x3ad)[0x7f30e64b122d]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f30e5e0ba15]
/usr/bin/python[0x400791]
=== Memory map: 
0040-00401000 r-xp  09:06 1181836
/usr/bin/python2.7
0060-00601000 r--p  09:06 1181836
/usr/bin/python2.7
00601000-00602000 rw-p 1000 09:06 1181836
/usr/bin/python2.7
00e65000-01a25000 rw-p  00:00 0
[heap]
404f9000-40596000 rw-p  00:00 0
41954000-41956000 r-xs  09:08 19
/tmp/gleT7vZR (deleted)
7f30dd223000-7f30dd423000 rw-s 7661eb000 00:05 593
/dev/nvidia0
7f30dd423000-7f30dd623000 rw-s 59aad7000 00:05 593
/dev/nvidia0
7f30dd623000-7f30dd823000 rw-s 6072fa000 00:05 593
/dev/nvidia0
7f30dd823000-7f30dd923000 rw-s 506579000 00:05 593
/dev/nvidia0
7f30dd923000-7f30dd92a000 rw-s 5176ff000 00:05 593
/dev/nvidia0
7f30dd92a000-7f30dd94a000 rw-s d006 00:05 593
/dev/nvidia0
7f30dd94a000-7f30dd98a000 rw-s 574b37000 00:05 593
/dev/nvidia0
7f30dd98a000-7f30dd9aa000 rw-s 56bbd3000 00:05 593
/dev/nvidia0
7f30dd9aa000-7f30dd9ea000 rw-s 6d1e49000 00:05 593
/dev/nvidia0
7f30dd9ea000-7f30ddaa2000 rw-p  00:00 0
7f30ddaa2000-7f30ddaa5000 r-xp  09:06 1058995
/usr/lib64/python2.7/lib-dynload/fcntl.so
7f30ddaa5000-7f30ddca4000 ---p 3000 09:06 1058995
/usr/lib64/python2.7/lib-dynload/fcntl.so
7f30ddca4000-7f30ddca5000 r--p 2000 09:06 1058995
/usr/lib64/python2.7/lib-dynload/fcntl.so
7f30ddca5000-7f30ddca6000 rw-p 3000 09:06 1058995
/usr/lib64/python2.7/lib-dynload/fcntl.so
7f30ddca6000-7f30ddcc1000 r-xp  09:06 1059009
/usr/lib64/python2.7/lib-dynload/_io.so
7f30ddcc1000-7f30ddec1000 ---p 0001b000 09:06 1059009
/usr/lib64/python2.7/lib-dynload/_io.so
7f30ddec1000-7f30ddec2000 r--p 0001b000 09:06 1059009
/usr/lib64/python2.7/lib-dynload/_io.so
7f30ddec2000-7f30ddecb000 rw-p 0001c000 09:06 1059009
/usr/lib64/python2.7/lib-dynload/_io.so
7f30ddecb000-7f30ddecf000 r-xp  09:06 1059019
/usr/lib64/python2.7/lib-dynload/zlib.so
7f30ddecf000-7f30de0ce000 ---p 4000 09:06 1059019
/usr/lib64/python2.7/lib-dynload/zlib.so
7f30de0ce000-7f30de0cf000 r--p 3000 09:06 1059019
/usr/lib64/python2.7/lib-dynload/zlib.so
7f30de0cf000-7f30de0d1000 rw-p 4000 09:06 1059019
/usr/lib64/python2.7/lib-dynload/zlib.so
7f30de0d1000-7f30de253000 rw-p  00:00 0
7f30de253000-7f30de25b000 r-xp  09:06 1058997
/usr/lib64/python2.7/lib-dynload/operator.so
7f30de25b000-7f30de45a000 ---p 8000 09:06 1058997
/usr/lib64/python2.7/lib-dynload/operator.so
7f30de45a000-7f30de45b000 r--p 7000 09:06 1058997
/usr/lib64/python2.7/lib-dynload/operator.so
7f30de45b000-7f30de45d000 r

Re: [PyMOL] command question RE printing out distances to text file

2014-06-09 Thread Robert Campbell

Hi Suzanne,

You can also get the distance printed in the external GUI or terminal window
by using the "cmd.distance" version of the command.  So either you can
assign the distance to a variable and print it or you can print the result
directly.

Assuming you have two selections, sele1 and sele2 specifying the atoms of
interest you can do:

  d = cmd.distance(sele1,sele2)
  print sele1,sele2,d


Cheers,
Rob

On Mon, 2014-06-09
13:13 EDT, Thomas Holder  wrote:

> Hi Suzanne,
> 
> you can use the get_distance command. It doesn't generate a distance
> object but prints the distance to the external window.
> 
> http://pymolwiki.org/index.php/Get_Distance
> 
> Cheers,
>   Thomas
> 
> On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC)
>  wrote:
> 
> > Fellow Pymol Users:
> > I may have asked this question before...but if so have forgotten. I am
> > measuring distances between 2 atoms in 2 different objects using the
> > distance command, and it is working perfectly, but I wonder if there is
> > a command I can use/add so that those distances can be printed in the
> > external gui as well as being shown in the viewer. I will be doing lots
> > of these at the same time and the screen will get crowded. Thank you in
> > advance.
> 




-- 
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
http://pldserver1.biochem.queensu.ca/~rlc

--
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Re: [PyMOL] command question RE printing out distances to text file

2014-06-09 Thread Robert Campbell

Hi Suzanne,

You can also get the distance printed in the external GUI or terminal window
by using the "cmd.distance" version of the command.  So either you can
assign the distance to a variable and print it or you can print the result
directly.

Assuming you have two selections, sele1 and sele2 specifying the atoms of
interest you could do something like this:

  d = cmd.distance(sele1,sele2)
  print sele1,sele2,d


Cheers,
Rob

On Mon, 2014-06-09
13:13 EDT, Thomas Holder  wrote:

> Hi Suzanne,
> 
> you can use the get_distance command. It doesn't generate a distance
> object but prints the distance to the external window.
> 
> http://pymolwiki.org/index.php/Get_Distance
> 
> Cheers,
>   Thomas
> 
> On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC)
>  wrote:
> 
> > Fellow Pymol Users:
> > I may have asked this question before...but if so have forgotten. I am
> > measuring distances between 2 atoms in 2 different objects using the
> > distance command, and it is working perfectly, but I wonder if there is
> > a command I can use/add so that those distances can be printed in the
> > external gui as well as being shown in the viewer. I will be doing lots
> > of these at the same time and the screen will get crowded. Thank you in
> > advance.
> 




-- 
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
http://pldserver1.biochem.queensu.ca/~rlc

--
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Re: [PyMOL] problem creating a 2D shape from pymol 3D structure using poseview.py

2014-06-09 Thread Thomas Holder

Hi Maryam,

the get_viewport command was added in PyMOL 1.5, so I guess you are using an 
older version and upgrading will solve your problem.

Cheers,
  Thomas

On 06 Jun 2014, at 21:30, M. Faridounnia  wrote:

> Dear Pymolers,
> 
> I was trying to run the posview.py downloaded from pymolwiki 
> (http://www.pymolwiki.org:/index.php/PoseView) but when I try to run the 
> script it gives this lines with the module error on get_viewport. I tried to 
> File 
> "/Volumes/Data/scm/vikki/bld/MacPyMOL.app/pymol/modules/pymol/parser.py", 
> line 254, in parse
>   File "/Volumes/Home/Users/.../pymol/poseview.py", line 49, in poseview
> viewport = cmd.get_viewport()
> AttributeError: 'module' object has no attribute 'get_viewport
> 
> I would appreciate if someone helps me understand this.
> 
> Best regards,
> Maryam

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.


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Re: [PyMOL] command question RE printing out distances to text file

2014-06-09 Thread Thomas Holder

Hi Suzanne,

you can use the get_distance command. It doesn't generate a distance object but 
prints the distance to the external window.

http://pymolwiki.org/index.php/Get_Distance

Cheers,
  Thomas

On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC)  
wrote:

> Fellow Pymol Users:
> I may have asked this question before...but if so have forgotten. I am 
> measuring distances between 2 atoms in 2 different objects using the distance 
> command, and it is working perfectly, but I wonder if there is a command I 
> can use/add so that those distances can be printed in the external gui as 
> well as being shown in the viewer. I will be doing lots of these at the same 
> time and the screen will get crowded. Thank you in advance.

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.


--
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Re: [PyMOL] command question RE printing out distances to text file

Re: [PyMOL] Visualize Sheets from C-alpha Only Structure

[PyMOL] Pymol startup error

Re: [PyMOL] command question RE printing out distances to text file

Re: [PyMOL] command question RE printing out distances to text file

Re: [PyMOL] problem creating a 2D shape from pymol 3D structure using poseview.py

Re: [PyMOL] command question RE printing out distances to text file

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