Re: [PyMOL] 3D Stereo Problem
Hi Deepangi, 1. OS: Windows 7 2. Monitor:Samsung Syncmaster 2233RZ 22in 3D Gaming LCD 3. Card: EVGA GeForce 9800 GTX+ 512MB PCIe w/Dual Link DVI 4. Glasses: NVIDIA 3D Vision Glasses Wrong graphics card: http://www.nvidia.com/object/quadro_pro_graphics_boards.html /Jesper -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] 3D Stereo Problem
On Wed, Jan 20, 2010 at 9:35 AM, Jesper Lykkegaard Karlsen je...@bioxray.au.dk wrote: Hi Deepangi, 1. OS: Windows 7 2. Monitor:Samsung Syncmaster 2233RZ 22in 3D Gaming LCD 3. Card: EVGA GeForce 9800 GTX+ 512MB PCIe w/Dual Link DVI 4. Glasses: NVIDIA 3D Vision Glasses Wrong graphics card: http://www.nvidia.com/object/quadro_pro_graphics_boards.html No according to this http://www.nvidia.com/object/3D_Vision_Requirements.html and an old post from the list http://bit.ly/61Lwbn. /Jesper -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] 3D Stereo Problem
Hi Marius Marius Retegan wrote: No according to this http://www.nvidia.com/object/3D_Vision_Requirements.html and an old post from the list http://bit.ly/61Lwbn. I thought this question was about getting pymol to run in 3D on win7. Not get your directX games to run in 3D. Pymol run OpenGL in a window and requires quad buffered stereo capable graphic cards (quadro and FireGL) to show 3D. Since this example is through Nvidia's 3D vision a quadro card is a MUST. /Jesper -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
Hi Jason, I think the number one feature I would like to see is eMovie incorporated into the standard build of PyMOL. The built in movie making facilities in PyMOL may be powerful but the scripting is a bit beyond those of us biologists who use computers especially if one is trying to make longer and more involved movies. eMovie is a really nice and easy to understand interface that is only spoiled by how buggy it is (especially on a Mac where it seems to disagree violently with the video card/chips). Secondly, more and more academic structural biologists use Macs - at the recent British Crystallographic Association winter meeting ten out of twelve speakers used Macs. If Mac support is decreased it will stop being used by academics. Finally, although I understand the reasons for PyMOL being sold to Schrodinger, I have to admit I was disappointed as in the past I have found Schrodinger singularly unhelpful in making their software available free(ish) to academics. I really really hope that all the great stuff in PyMOL isn't stolen for other applications whilst PyMOL itself is left to wither away. Simon On 20 Jan 2010, at 04:26, Jason Vertrees wrote: PyMOLers, We need to move forward on PyMOL development, so I'm collecting ideas from all our users on what they most want in future versions of PyMOL. We already have a page on the PyMOL wiki for this (http://pymolwiki.org/index.php/Ideas) from 2008/2009. We can discuss the ideas here and on the wiki; this list is more for two-way communication and the wiki for one-way. If you have a specific request for an enhancement you can also email it directly to h...@schrodinger.com; please put PyMOL in the subject so I can get them easily. Each request submitted will be considered for implementation. Last, you're particularly passionate about your feature request, email me directly and we can chat about it via phone/skype. Thanks, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol- us...@lists.sourceforge.net -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Feature Requests/Ideas (Sean Law)
Hi! 1) Ever since I have used the ray function in PyMOL i ran into problems creating the right resolution/size of the ray trace images for posters/papers. I know its just a matter of x/y pixel settings, but every time i had to look it up again. However i wrote a little script embedded in the BNI-Tools plugin, where one easily can set the size and resolution of the ray trace image. Of course it would be nice to have VG, but maybe it is a meantime solution. Load the BNI-Tools install it as plug-in and get to Plugin--BNI PyMOLl Tools --Create -- ray --set and input the width-size in millimetre (mm) and the resolution (in dpi) you want to have. (or you can select a pre-set) 3) I have no solution for MD trajectories but BNI-Tools can also be used to import multiple pdb files (like snapshots) into the same object using different states. (The object is named like the first read in) Maybe it is useful to you. BNI PyMOLl Tools -- Load Files -- Multiple Files into states There is currently no user guide for BNI-Tools but most of the BNI-Tools commands act on the (sele) selection. If you want to give BNI-Tools a try download it from http://sourceforge.net/projects/bni-tools/ and experiment with it. Its not a completely bug-free version, so any bug-reports and suggestions are welcome. Regards, Georg -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] get translation / rotation matrix from super
Matthias, Good thinking. Nice workaround. -- Jason On Wed, Jan 20, 2010 at 2:54 AM, Matthias Haffke matze_haf...@hotmail.com wrote: Thanks for your help Jason and David! I'll have a look at your suggestions, although I solved my problem in a different way. I just copied the coordinates of the important symmetry mates into the pdb file containing the original molecule of protein B (and set up a new chain for each of the sym mates). Superimposing protein B (the chain containing the original molecule) on protein A moves all desired sym mates according to the movement of the original molecule. Anyway, getting the translation / rotation matrix is much more convenient than copying all the coordinates... :-) Thanks once again! Matthias Date: Tue, 19 Jan 2010 07:02:44 -0800 From: dwash59_2...@yahoo.com Subject: Re: [PyMOL] get translation / rotation matrix from super To: matze_haf...@hotmail.com; pymol-users@lists.sourceforge.net Matthias Haffke said: Is there a way to extract the translation / rotation matrix out of the super command or can I use another command to align both, protein B and A and to apply the function on every symmetry mate? In addition the commands mentioned by Jason, you can look at matrix_copy http://www.pymolwiki.org/index.php/Matrix_copy You would align protein B to A, then matrix_copy protein_b, symmetry_mates Note, the second argument can have a wild card, so you only need to call the command once to move all of them if they all have a common prefix or the such. -David Dein Santa Claus hat rote Augen? Jetzt X-Mas-Fotos bearbeiten! -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Getting information fron selected objects
I am writing a Pymol plugin, in which I need to extract, manipulate, and replace the coordinates of selected atoms. Are there examples out there I could use as a prototype? For starters, what command(s) do I use to get the name strings of residues that I've selected with mouse clicks. I would like to assign these to a variable. Then the same question applies to coordinates. How do I assign the values of atomic coordinates to a list variable in my plug_in script? -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] New Feature Ideas
Hi Jason, here are two minor improvements: 1) set pdb_mirror option to be able to use a European (EBI) mirror for example. The RCSB mirror is rather slow from Europe. 2) uppercase support for fetch_path; currently only lowercase file names are loaded. Something more challenging: 3) Export scenes as webGL.This is a bit more ambitious to be honest but the benefits could be huge. A couple of problems could be solved at once, such as integration into web pages or documents, mobile devices, etc. without any plugins or Java stuff. Adrian -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
- Original Message From: Adrian Schreyer ams...@cam.ac.uk To: jason.vertr...@schrodinger.com; PyMOL-users@lists.sourceforge.net Sent: Wed, January 20, 2010 10:00:03 AM Subject: [PyMOL] New Feature Ideas Something more challenging: 3) Export scenes as webGL.This is a bit more ambitious to be honest but the benefits could be huge. A couple of problems could be solved at once, such as integration into web pages or documents, mobile devices, etc. without any plugins or Java stuff. Adrian +1000 People really need to jump on the bandwagon of getting rid of Java plugins. I wish the pdb het atom pages would get rid of JMol for 3D viewing of molecules and hop onto twirlymol. Just as a question, what version of OpenGL does pymol rely on? WebGL is based around OpenGL ES 2.0 which is based around OpenGL 2.0. I assume pymol doesn't use OpenGL 3.0, since its not even in OS X right now. This area is something I'm hugely ignorant of though. -David -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
Two items come to mind: 1. A Powerpoint plugin for live Pymol viewing in presentations. 2. A simpler method of doing structure morphs in Pymol. Intelligent morphing is incredibly powerful for visualizing protein conformational changes based on "endpoint" protein structures, or just evaluating/understanding the differences between point mutations of proteins. I think both of these were on the radar screen for Pymol feature enhancement at some point in the recent past. Cheers. On 1/19/2010 11:26 PM, Jason Vertrees wrote: PyMOLers, We need to move forward on PyMOL development, so I'm collecting ideas from all our users on what they most want in future versions of PyMOL. We already have a page on the PyMOL wiki for this (http://pymolwiki.org/index.php/Ideas) from 2008/2009. We can discuss the ideas here and on the wiki; this list is more for two-way communication and the wiki for one-way. If you have a specific request for an enhancement you can also email it directly to h...@schrodinger.com; please put "PyMOL" in the subject so I can get them easily. Each request submitted will be considered for implementation. Last, you're particularly passionate about your feature request, email me directly and we can chat about it via phone/skype. Thanks, -- Jason -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] new ideas
Hi Jason I need such features. I open two different pdbs and I want to manually move one structure relative to another. I want to dock one structure into another or superpose 2 structures manually. Is it possible? Or I want to move a fragment of the molecule relative to the rest of the molecule. Is it possible? Maia -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Getting information fron selected objects
Phil, The answers to your questions lie in the iterate, iterate_state, alter, and alter_state commands. The PyMOLWiki has extensive documentation on these commands (http://pymolwiki.org/index.php/Iterate). Once you select something with the mouse you can get information using iterate/alter. # make mouse selection; the (sele) selection is created # create a copy selection called myCopy select myCopy, (sele) # count atoms in myCopy print cmd.count_atoms(myCopy) # see what atom IDs are in the selection iterate myCopy, print ID Hope this helps, -- Jason On Tue, Jan 19, 2010 at 2:00 PM, Phil Payne Local ppa...@maxwell.compbio.ucsf.edu wrote: I am writing a Pymol plugin, in which I need to extract, manipulate, and replace the coordinates of selected atoms. Are there examples out there I could use as a prototype? For starters, what command(s) do I use to get the name strings of residues that I've selected with mouse clicks. I would like to assign these to a variable. Then the same question applies to coordinates. How do I assign the values of atomic coordinates to a list variable in my plug_in script? -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] launching pymol from a script
Hi there,
Please, did someone check that? It would be very appreciated.
Thanks
Alan
On Mon, Jan 4, 2010 at 16:49, Alan alanwil...@gmail.com wrote:
Hi there,
I use both pymol via Fink (on MBP 10.6.2) all in 64 bits and MacPymol 1.2r3
(licensed to PDBe).
Both work fine but I tried
http://pymolwiki.org/index.php/Launching_From_a_Script
with
1) export PYTHONPATH=/Applications/MacPyMOL.app/pymol/modules
2) export PYTHONPATH=/sw/lib/pymol-py26/modules
and running 'launch_pymol.sh' script that contains:
#!/usr/bin/env python
# Tell PyMOL we don't want any GUI features.import
__mainmain__.pymol_argv = [ 'pymol', '-Gi' ]
# Importing the PyMOL module will create the window.
import pymol
# Call the function below before using any PyMOL modules.
pymol.finish_launching()
from pymol import cmdcmd.stereo('walleye')cmd.set('stereo_shift',
0.23)cmd.set('stereo_angle', 1.0)
and I got for:
1) amadeus[2027]:~/TMP% ./pymol.sh
Traceback (most recent call last):
File ./pymol.sh, line 9, in module
import pymol
File /Applications/MacPyMOL.app/pymol/modules/pymol/__init__.py, line
472, in module
import _cmd
ImportError: No module named _cmd
2) amadeus[2029]:~/TMP% ./pymol.sh
Xlib: extension XFree86-VidModeExtension missing on display
/tmp/launch-35V4Bz/:0.
freeglut (pymol): XF86VidModeGetViewPort failed
Xlib: extension XFree86-VidModeExtension missing on display
/tmp/launch-35V4Bz/:0.
freeglut (pymol): XF86VidModeGetModeLine failed
freeglut (pymol): failed to change screen settings
PyMOL(TM) Molecular Graphics System, Version 1.2r3pre.
Copyright (C) 2009 by DeLano Scientific 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.
[1]25649 segmentation fault ./pymol.sh
Would someone know what else I can try to do?
Many thanks in advance,
Alan
--
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
--
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev___
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Re: [PyMOL] Feature Requests/Ideas (Sean Law)
Georg, Thanks for the reply. My comments are below. 1) Ever since I have used the ray function in PyMOL i ran into problems creating the right resolution/size of the ray trace images for posters/papers. I know its just a matter of x/y pixel settings, but every time i had to look it up again. However i wrote a little script embedded in the BNI-Tools plugin, where one easily can set the size and resolution of the ray trace image. Of course it would be nice to have VG, but maybe it is a meantime solution. Load the BNI-Tools install it as plug-in and get to Plugin--BNI PyMOLl Tools --Create -- ray --set and input the width-size in millimetre (mm) and the resolution (in dpi) you want to have. (or you can select a pre-set) So you'd like to see something like: ray 10cm, 20cm, dpi=300? ray 2.5in, 5in, dpi=300? 3) I have no solution for MD trajectories but BNI-Tools can also be used to import multiple pdb files (like snapshots) into the same object using different states. (The object is named like the first read in) Maybe it is useful to you. BNI PyMOLl Tools -- Load Files -- Multiple Files into states This is easily achieved using a mixture of Python and the PyMOL API. Let's assume you have a 100 files in a directory, all trajectory snapshots. To load all 100 objects into one PyMOL object, just do: import glob for x in glob.glob(yourDirectoryName/*.pdb): cmd.load(x, myMultiStateObject) PyMOL know that if you load more than one structure into the same object name, to make it a multistate object. -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
Adrian, My comments follow. 1) set pdb_mirror option to be able to use a European (EBI) mirror for example. The RCSB mirror is rather slow from Europe. This is a good idea; allowing people to set their own server. 2) uppercase support for fetch_path; currently only lowercase file names are loaded. Do you mean the PDB ids are all lower case or the fetch_paths themselves? One caveat for paths is the cross-platform inconsistency in path naming: Windows and some Apple systems are case insensitive. Something more challenging: 3) Export scenes as webGL.This is a bit more ambitious to be honest but the benefits could be huge. A couple of problems could be solved at once, such as integration into web pages or documents, mobile devices, etc. without any plugins or Java stuff. Interesting. -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Feature Requests/Ideas (Sean Law)
Hi, ray 10cm, 20cm, dpi=300? ray 2.5in, 5in, dpi=300? I'd slightly modify that to read: ray 10,10,units=cm,resolution=300 where units can be pixels (default), cm, inches, meters, yards, lightyears... Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
Roger, Both of these features are available to PyMOL subscribers already. You can get AxPyMOL which has the ActiveX plugin for PowerPoint. There is no need to tab out of your presentation. Also in the incentive version is RigiMOL the molecular morpher. We could probably clean up the interface for this, as currently you have to be able to do simple Python programming. Warren went through alot of work to realize these two features, which is why he charged for them. Once I rebuild the AxPyMOL builds you can test out the demo version. If you have an immediate need for AxPyMOL, please contact me directly and I might be able to push out that Eval build more quickly. Thanks, -- Jason On Wed, Jan 20, 2010 at 11:08 AM, Roger Rowlett rrowl...@colgate.edu wrote: Two items come to mind: 1. A Powerpoint plugin for live Pymol viewing in presentations. 2. A simpler method of doing structure morphs in Pymol. Intelligent morphing is incredibly powerful for visualizing protein conformational changes based on endpoint protein structures, or just evaluating/understanding the differences between point mutations of proteins. I think both of these were on the radar screen for Pymol feature enhancement at some point in the recent past. Cheers. On 1/19/2010 11:26 PM, Jason Vertrees wrote: PyMOLers, We need to move forward on PyMOL development, so I'm collecting ideas from all our users on what they most want in future versions of PyMOL. We already have a page on the PyMOL wiki for this (http://pymolwiki.org/index.php/Ideas) from 2008/2009. We can discuss the ideas here and on the wiki; this list is more for two-way communication and the wiki for one-way. If you have a specific request for an enhancement you can also email it directly to h...@schrodinger.com; please put PyMOL in the subject so I can get them easily. Each request submitted will be considered for implementation. Last, you're particularly passionate about your feature request, email me directly and we can chat about it via phone/skype. Thanks, -- Jason -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] PyMOL on the Mac
PyMOLers, I just want to quickly reiterate: PyMOL will still be supported on the Mac--no need to worry. Even though other Schrodinger software doesn't run on the Mac, PyMOL will. MacPyMOL will live on. Best, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Feature Requests/Ideas (Sean Law)
Several more votes for one of these from lots of people in my lab. On Wed, Jan 20, 2010 at 3:54 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi, ray 10cm, 20cm, dpi=300? ray 2.5in, 5in, dpi=300? I'd slightly modify that to read: ray 10,10,units=cm,resolution=300 where units can be pixels (default), cm, inches, meters, yards, lightyears... Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Feature Requests/Ideas (Sean Law)
That seems like a modification that makes it less flexible. Now I can't do: ray 2.5in, 20cm, dpi=300 Don't ask me why I might want to use two different units, I just don't see a reason to make it so I cannot. I'm frequently surprised by my desires. And resolution is inconsistent with the png function, and less precise. I don't know what units I have with the resolution argument. One of my high ranking complaints about pymol has been certain inconsistencies in the api, so that's actually what I care about more. (Maybe I should write those up, but fixing these things is always hard because backwards compatibility kind of matters). Also, it would be nice to have this in the png function as well. As for units, I thought it would be nice to read the file used by the units unix type function (located at /usr/share/units.dat on my linux machine, /usr/share/misc/units.lib). Maybe ship with and support the mac/bsd one since that should be friendly with the pymol license and check for the system one at runtime. That way, if new units are ever invented, we get some (semi-)automatic support. -David - Original Message From: Tsjerk Wassenaar tsje...@gmail.com To: Jason Vertrees jason.vertr...@schrodinger.com Cc: Georg Steinkellner georg.steinkell...@uni-graz.at; pymol-users@lists.sourceforge.net Sent: Wed, January 20, 2010 3:54:25 PM Subject: Re: [PyMOL] Feature Requests/Ideas (Sean Law) Hi, ray 10cm, 20cm, dpi=300? ray 2.5in, 5in, dpi=300? I'd slightly modify that to read: ray 10,10,units=cm,resolution=300 where units can be pixels (default), cm, inches, meters, yards, lightyears... Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
1) I would love it if the PDB Loader Service Plugin would clean up what it left in /tmp on pymol exit. I have a feeling this might be complicated though. I just have a bad memory when I first entered this world and I had pymol open and I was trying to load a pdb and the plugin just would not work. The previous graduate student using the system had previously loaded the same pdb using the plugin and the file had written in /tmp and the PDB Loader would therefore not get me the file. When you're just starting a rotation in a new lab, that type of problem can scar you as you have to explain why it took you half an hour to open a pdb in pymol... An alternative solution is to check for the filename before trying to write there. And be like Firefox and just name them 1ACB-1.pdb when 1ACB.pdb can't be written to. 2) This might be out of your range as it is a plug in written by the community, but DynoPlot could become something really cool with a little love and care. My big problem right now is that you are only able to create a plot with a single selection. I teach a lab once a year where we have the students use dynoplot to make ramachandran plots of the helices, then they have to restart pymol before they can select the beta sheets and make a ramachandran plot of them as well. As we all know, losing a pymol session can be a painful experience. Having to restart is also rough. 3) A more extensive undo/redo system. It would be nice to be able to undo anything. And then redo it. I'm talking fetch 2no8; split_states, realizing there's 60 models and just doing undo and having a single model again. Or I accidentally change my view, I can go back. I don't know what level of granularity it should be, but something would be good. Again, losing that perfect view or such can be painful. -David - Original Message From: Jason Vertrees jason.vertr...@schrodinger.com To: pymol-users@lists.sourceforge.net Sent: Tue, January 19, 2010 11:26:39 PM Subject: [PyMOL] New Feature Ideas PyMOLers, We need to move forward on PyMOL development, so I'm collecting ideas from all our users on what they most want in future versions of PyMOL. We already have a page on the PyMOL wiki for this (http://pymolwiki.org/index.php/Ideas) from 2008/2009. We can discuss the ideas here and on the wiki; this list is more for two-way communication and the wiki for one-way. If you have a specific request for an enhancement you can also email it directly to h...@schrodinger.com; please put PyMOL in the subject so I can get them easily. Each request submitted will be considered for implementation. Last, you're particularly passionate about your feature request, email me directly and we can chat about it via phone/skype. Thanks, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] new ideas
Thanks, But I could not find the download site for FreeMol. Could somebody send me a link to FreeMol? Maia Jason Vertrees wrote: Maia, You can already move structures independently. If you install PyMOL+FreeMOL you can have access to the MMFF-enabled PyMOL that will allow you to do small molecule cleanup and editing. Try putting your mouse into Editing Mode and moving atoms around. It's not hard. Check this out: http://pymolwiki.org/index.php/Molecular_Sculpting for some help. Regards, -- Jason On Wed, Jan 20, 2010 at 11:52 AM, Maia Cherney ch...@ualberta.ca wrote: Hi Jason I need such features. I open two different pdbs and I want to manually move one structure relative to another. I want to dock one structure into another or superpose 2 structures manually. Is it possible? Or I want to move a fragment of the molecule relative to the rest of the molecule. Is it possible? Maia -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
David, Some good suggestions, but I think too localized to you, specifically. My comments follow. 1) I would love it if the PDB Loader Service Plugin would clean up what it left in /tmp on pymol exit. I have a feeling this might be complicated though. I just have a bad memory when I first entered this world and I had pymol open and I was trying to load a pdb and the plugin just would not work. The previous graduate student using the system had previously loaded the same pdb using the plugin and the file had written in /tmp and the PDB Loader would therefore not get me the file. When you're just starting a rotation in a new lab, that type of problem can scar you as you have to explain why it took you half an hour to open a pdb in pymol... First time I've heard this request. PyMOL attempts to cache the data, so you don't have to keep re-downloading the PDB files. Also, if PyMOL crashes or is suddenly killed, there's no way to clean up the remaining PDBs. Plus, there could be security issues with removing files: fetch '/bin/rm -r *' might allow for some kind of evilness. To be serious about this, many more people need to show interest in it. An alternative solution is to check for the filename before trying to write there. And be like Firefox and just name them 1ACB-1.pdb when 1ACB.pdb can't be written to. Maybe this smacks of a different solution altogether: project-based sessions? 2) This might be out of your range as it is a plug in written by the community, but DynoPlot could become something really cool with a little love and care. My big problem right now is that you are only able to create a plot with a single selection. I teach a lab once a year where we have the students use dynoplot to make ramachandran plots of the helices, then they have to restart pymol before they can select the beta sheets and make a ramachandran plot of them as well. As we all know, losing a pymol session can be a painful experience. Having to restart is also rough. You would have to work with the DynoPlot author to improve this. 3) A more extensive undo/redo system. It would be nice to be able to undo anything. And then redo it. I'm talking fetch 2no8; split_states, realizing there's 60 models and just doing undo and having a single model again. Or I accidentally change my view, I can go back. I don't know what level of granularity it should be, but something would be good. Again, losing that perfect view or such can be painful. This is a definite must, especially for molecular editing. In PyMOL, sadly, this is very hard. Warren fretted about this for months, and even started a basic level of undo. I predict this will be around after we do some major refactoring--possibly in PyMOL 2.0. :-) Thanks for your suggestions. -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] new ideas
In my incentive build, freemol is present with the following readme: This is a binary distribution of the FreeMOL Open-Source Compilation. The FreeMOL project home page can be found at: http://bioinformatics.org/freemol Complete source code for building FreeMOL and its various components can be browsed via: http://www.bioinformatics.org/websvn/listing.php?repname=freemol and fetched via: svn co svn://bioinformatics.org/svnroot/freemol/trunk Licensing information can be found in LICENSE.txt If you have any questions about FreeMOL, please contact: Warren L. DeLano, Ph.D. DeLano Scientific LLC war...@delsci.com Thank You! I don't have any instructions how to incorporate this into building from pymol trunk necessarily though. In the incentive builds, the freemol folder is not inside ext or modules or anything, but instead is a top level directory like those. You will have to build the sources of the things that come with it (apbs, mengine, mpeg_encode, pdb2pqr). I think pymol autodetects the presence of freemol based on this grep output on the pymol source. modules/pymol/__init__.py:# auto-detect bundled FREEMOL (if present) modules/pymol/__init__.py:if not os.environ.has_key(FREEMOL): modules/pymol/__init__.py:test_path = os.path.join(os.environ['PYMOL_PATH'],freemol) modules/pymol/__init__.py:os.environ['FREEMOL'] = test_path modules/pymol/__init__.py:# include FREEMOL's libpy in sys.path (if present) modules/pymol/__init__.py:if os.environ.has_key(FREEMOL): modules/pymol/__init__.py:freemol_libpy = os.path.join(os.environ['FREEMOL'],libpy) modules/pymol/__init__.py:if os.path.isdir(freemol_libpy): modules/pymol/__init__.py:if freemol_libpy not in sys.path: modules/pymol/__init__.py:sys.path.append(freemol_libpy) Hopefully this all helps. -David - Original Message From: Maia Cherney ch...@ualberta.ca To: Jason Vertrees jason.vertr...@schrodinger.com Cc: pymol-users@lists.sourceforge.net Sent: Wed, January 20, 2010 9:37:46 PM Subject: Re: [PyMOL] new ideas Thanks, But I could not find the download site for FreeMol. Could somebody send me a link to FreeMol? Maia Jason Vertrees wrote: Maia, You can already move structures independently. If you install PyMOL+FreeMOL you can have access to the MMFF-enabled PyMOL that will allow you to do small molecule cleanup and editing. Try putting your mouse into Editing Mode and moving atoms around. It's not hard. Check this out: http://pymolwiki.org/index.php/Molecular_Sculpting for some help. Regards, -- Jason On Wed, Jan 20, 2010 at 11:52 AM, Maia Cherney wrote: Hi Jason I need such features. I open two different pdbs and I want to manually move one structure relative to another. I want to dock one structure into another or superpose 2 structures manually. Is it possible? Or I want to move a fragment of the molecule relative to the rest of the molecule. Is it possible? Maia -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] new ideas
For the sale of PyMOL, we had to take down FreeMOL temporarily. I will put it back up soon. I think you can still get access to the code from bioinformatics.org. I'll update the list when I've posted the FreeMOL code. Thanks, -- Jason On Wed, Jan 20, 2010 at 10:27 PM, David Hall dwash59_2...@yahoo.com wrote: In my incentive build, freemol is present with the following readme: This is a binary distribution of the FreeMOL Open-Source Compilation. The FreeMOL project home page can be found at: http://bioinformatics.org/freemol Complete source code for building FreeMOL and its various components can be browsed via: http://www.bioinformatics.org/websvn/listing.php?repname=freemol and fetched via: svn co svn://bioinformatics.org/svnroot/freemol/trunk Licensing information can be found in LICENSE.txt If you have any questions about FreeMOL, please contact: Warren L. DeLano, Ph.D. DeLano Scientific LLC war...@delsci.com Thank You! I don't have any instructions how to incorporate this into building from pymol trunk necessarily though. In the incentive builds, the freemol folder is not inside ext or modules or anything, but instead is a top level directory like those. You will have to build the sources of the things that come with it (apbs, mengine, mpeg_encode, pdb2pqr). I think pymol autodetects the presence of freemol based on this grep output on the pymol source. modules/pymol/__init__.py: # auto-detect bundled FREEMOL (if present) modules/pymol/__init__.py: if not os.environ.has_key(FREEMOL): modules/pymol/__init__.py: test_path = os.path.join(os.environ['PYMOL_PATH'],freemol) modules/pymol/__init__.py: os.environ['FREEMOL'] = test_path modules/pymol/__init__.py: # include FREEMOL's libpy in sys.path (if present) modules/pymol/__init__.py: if os.environ.has_key(FREEMOL): modules/pymol/__init__.py: freemol_libpy = os.path.join(os.environ['FREEMOL'],libpy) modules/pymol/__init__.py: if os.path.isdir(freemol_libpy): modules/pymol/__init__.py: if freemol_libpy not in sys.path: modules/pymol/__init__.py: sys.path.append(freemol_libpy) Hopefully this all helps. -David - Original Message From: Maia Cherney ch...@ualberta.ca To: Jason Vertrees jason.vertr...@schrodinger.com Cc: pymol-users@lists.sourceforge.net Sent: Wed, January 20, 2010 9:37:46 PM Subject: Re: [PyMOL] new ideas Thanks, But I could not find the download site for FreeMol. Could somebody send me a link to FreeMol? Maia Jason Vertrees wrote: Maia, You can already move structures independently. If you install PyMOL+FreeMOL you can have access to the MMFF-enabled PyMOL that will allow you to do small molecule cleanup and editing. Try putting your mouse into Editing Mode and moving atoms around. It's not hard. Check this out: http://pymolwiki.org/index.php/Molecular_Sculpting for some help. Regards, -- Jason On Wed, Jan 20, 2010 at 11:52 AM, Maia Cherney wrote: Hi Jason I need such features. I open two different pdbs and I want to manually move one structure relative to another. I want to dock one structure into another or superpose 2 structures manually. Is it possible? Or I want to move a fragment of the molecule relative to the rest of the molecule. Is it possible? Maia -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
[PyMOL] Feature Requests Hint
PyMOLers, Just a quick note: if you're on the list and see a feature you like, please reply to that email with a quick yea vote. It's even better if you let us know why you like it. Silence regarding a feature only down-weights its perceived importance. Thanks, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
