Re: [PyMOL] feature request: supercell construction
Hi Nick,
I recently was playing with (aka learning) the crystallographic symmetry
information in PDB files and now took your feature request as an
exercise. See attached file, hope it does what you had in mind.
Cheers,
Thomas
On Mon, 2010-04-12 at 14:12 -0600, Nicolas Bock wrote:
It would be great if pymol had support for constructing and displaying
a supercell:
For data files that support crystallographic information, e.g. pdb,
pymol can already display the unit cell (show cell). It would be great
if one could easily display multiple copies of the unit cell, along
the lines of
supercell 1,1,2
where pymol would then copy the unit cell along the c-axis and display
2 unit cells.
supercell 2,2,2
would display 2 copies along the a, b, and c axes, and display 8 unit
cells in total.
As a related request it would be great if pymol could construct a unit
cell in case the crystallographic information in the input file does
not exist. This could come in handy for instance when reading from
xyz. Maybe a command such as
construct_supercell a=10.2, b=10.2, c=15, alpha=90.0, beta=90,
gamma=90
would construct a cubic cell with dimensions axbxc.
Thanks,
nick
'''
(c) 2010 Thomas Holder
PyMOL python script (load with `run supercell.py`)
Usage: See help supercell
'''
from pymol import cmd, cgo
from math import cos, sin, radians, sqrt
import numpy
def cellbasis(angles, edges):
'''
For the unit cell with given angles and edge lengths calculate the basis
transformation (vectors) as a 4x4 numpy.array
'''
rad = [radians(i) for i in angles]
basis = numpy.identity(4)
basis[0][1] = cos(rad[2])
basis[1][1] = sin(rad[2])
basis[0][2] = cos(rad[1])
basis[1][2] = (cos(rad[0]) - basis[0][1]*basis[0][2])/basis[1][1]
basis[2][2] = sqrt(1 - basis[0][2]**2 - basis[1][2]**2)
edges.append(1.0)
return basis * edges # numpy.array multiplication!
def supercell(a=1, b=1, c=1, object=None, color='blue'):
'''
DESCRIPTION
Draw a supercell, as requested by Nicolas Bock on the pymol-users
mailing list (Subject: [PyMOL] feature request: supercell construction
Date: 04/12/2010 10:12:17 PM (Mon, 12 Apr 2010 14:12:17 -0600))
USAGE
supercell a, b, c [, object [, color]]
ARGUMENTS
a, b, c = integer: repeat cell in x,y,z direction a,b,c times
{default: 1,1,1}
object = string: name of object to take cell definition from
color = string: color of cell {default: blue}
SEE ALSO
show cell
'''
if object is None:
object = cmd.get_object_list()[0]
sym = cmd.get_symmetry(object)
cell_edges = sym[0:3]
cell_angles = sym[3:6]
basis = cellbasis(cell_angles, cell_edges)
assert isinstance(basis, numpy.ndarray)
ts = list()
for i in range(int(a)):
for j in range(int(b)):
for k in range(int(c)):
ts.append([i,j,k])
obj = [
cgo.BEGIN,
cgo.LINES,
cgo.COLOR,
]
obj.extend(cmd.get_color_tuple(color))
for t in ts:
shift = basis[0:3,0:3] * t
shift = shift[:,0] + shift[:,1] + shift[:,2]
for i in range(3):
vi = basis[0:3,i]
vj = [
numpy.array([0.,0.,0.]),
basis[0:3,(i+1)%3],
basis[0:3,(i+2)%3],
basis[0:3,(i+1)%3] + basis[0:3,(i+2)%3]
]
for j in range(4):
obj.append(cgo.VERTEX)
obj.extend((shift + vj[j]).tolist())
obj.append(cgo.VERTEX)
obj.extend((shift + vj[j] + vi).tolist())
cmd.load_cgo(obj, 'supercell')
cmd.extend('supercell', supercell)
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[PyMOL] pyMol executing python script: file path
Dear pyMol users, I am developing a python script for pyMol. If a user clicks File-Run and selects the script (for example c:/test/myScript.py), how do I determine the path of the script, i.e. (c:/test/) from inside the running script? I tried various python possibilities (os.path.abspath(__file__), inspect.getfile(sys._getframe(1))), all of them point to the pyMol __init__.py file which is not what I need. Thank you. Petr Benes. -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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 request: supercell construction
Hi Thomas, thanks! I noticed a few things: - when I run supercell 2, 1, 1 I get another cell outline along the a axis, but no atoms are shown in the second cell. Do I have to run another command for them to show up? - when I run the command again with other values for a, b, or c, nothing changes. I would expect that running the sequence supercell 2, 1, 1 and then supercell 2, 2, 1 would show me a 2x2x1 supercell at the end, but I see only the 2x1x1 supercell. Thanks again, nick On Wed, Apr 14, 2010 at 03:24, Thomas Holder tho...@thomas-holder.dewrote: Hi Nick, I recently was playing with (aka learning) the crystallographic symmetry information in PDB files and now took your feature request as an exercise. See attached file, hope it does what you had in mind. Cheers, Thomas On Mon, 2010-04-12 at 14:12 -0600, Nicolas Bock wrote: It would be great if pymol had support for constructing and displaying a supercell: For data files that support crystallographic information, e.g. pdb, pymol can already display the unit cell (show cell). It would be great if one could easily display multiple copies of the unit cell, along the lines of supercell 1,1,2 where pymol would then copy the unit cell along the c-axis and display 2 unit cells. supercell 2,2,2 would display 2 copies along the a, b, and c axes, and display 8 unit cells in total. As a related request it would be great if pymol could construct a unit cell in case the crystallographic information in the input file does not exist. This could come in handy for instance when reading from xyz. Maybe a command such as construct_supercell a=10.2, b=10.2, c=15, alpha=90.0, beta=90, gamma=90 would construct a cubic cell with dimensions axbxc. Thanks, nick -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] pyMol executing python script: file path
Petr, This is a cool problem treading on the grounds of PyMO/Python/System integration. You could create a wrapper function that takes the absolute path to the file, then chdir to the directory with the file, and import the file. Once you os.chdir somewhere, cmd.pwd() should return the new directory. Also, instead of importing the file you could os.chdir to the directory and then to cmd.do(run %s % fileName). Here's an example of the former idea: import os from os import path def myRun(fileName): p=path.dirname(fileName) f=path.basename(fileName) if f.endswith(.py): f = f[:-3] os.chdir(p) # import using a string __import__(f) To test, create a python script called a.py in /tmp and run with, myRun(/tmp/a.py) You could extend the above to run a specific function within your file. Cheers, -- Jason On Wed, Apr 14, 2010 at 2:53 AM, Petr Benes 60...@mail.muni.cz wrote: Dear pyMol users, I am developing a python script for pyMol. If a user clicks File-Run and selects the script (for example c:/test/myScript.py), how do I determine the path of the script, i.e. (c:/test/) from inside the running script? I tried various python possibilities (os.path.abspath(__file__), inspect.getfile(sys._getframe(1))), all of them point to the pyMol __init__.py file which is not what I need. Thank you. Petr Benes. -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] RMSD for ALL ATOMS against ALL ATOMS
Hi All Pymol users I have a set of 40 X-ray crystallographic structures complexed with inhibitors belonging to a specific family of kinases. Binding site residues within 5 angstrom from the inhibitor were selected for each PDB structure and saved separately. Now i have a set of 40 PDB files which has only the binding site residues. I want to perform RMSD for ALL ATOMS against ALL ATOMS. The first structure should be fixed and compared with the remaining 39 structures. For the next time, second structure is fixed and so on for all the 40 structures. Literally it should look like a 40X40 matrix table. I used align, fit and rms commands. Each one gives different values. Which is the best? Can you help me? Thank you in advanceRenuka -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] Res: Res: Pymol 64-bits MacOSX
Hi Jason, Sorry for taking that long to answer you, I was out of town. Well the picture that I have has 1441X814 pixels, which is way below your 4000X4000 pixels. I don't believe the resolution is the issue here but the complexity of the scene - I am trying to ray four big proteins (the complex formed by them is around 200kd) and a short stretch of DNA (40bp). Furthermore, I just don't want to ray only the cartoon, but the the cartoon together with the surface - pymol rays perfectly the cartoon but when I add the surface it becomes memory-demanding. Thank you, Lucas - Mensagem original De: Jason Vertrees jason.vertr...@schrodinger.com Para: Lucas Santos lusasan...@yahoo.com.br Cc: pymol-users@lists.sourceforge.net Enviadas: Sexta-feira, 9 de Abril de 2010 17:29:24 Assunto: Re: [PyMOL] Res: Pymol 64-bits MacOSX Lucas, How many pixels in your image? Also, how complex are your scenes? I've managed to pump out images at 4000x4000 (16,000,000 pixels). We can probably go larger, with some effort. What resolutions and complexities have others managed? Cheers, -- Jason On Fri, Apr 9, 2010 at 2:45 PM, Lucas Santos lusasan...@yahoo.com.br wrote: Hi, I tried to change the hash_max but it still crashing, I guess the images are quite big. Anyway, I will try to install PyMol under snow leopard (I got the disk but haven't installed yet). Thank you all for the help! Cheers, Lucas - Mensagem original De: Jason Vertrees jason.vertr...@schrodinger.com Para: Lucas Santos lusasan...@yahoo.com.br Cc: pymol-users@lists.sourceforge.net Enviadas: Sexta-feira, 9 de Abril de 2010 11:45:23 Assunto: Re: [PyMOL] Pymol 64-bits MacOSX Lucas, Try reducing your hash_max setting (http://www.pymolwiki.org/index.php/Hash_max). This will may ray tracing slower, but allows for larger images. Also, 64-bit MacPyMOL does not yet exist; we're still waiting on Tcl/Tk to update to 64-bit Carbon/Cocoa as they're using 32-bit now which is what our Pmw is built against. Cheers, -- Jason On Fri, Apr 9, 2010 at 11:22 AM, Lucas Santos lusasan...@yahoo.com.br wrote: Hi there, I have been facing some memory problems with macpymol 32-bits lately. When I try to ray a couple of big images my pymol crashes (malloc error), issue that could be easily fixed just by using a 64-bit pymol version - physical memory is not an issue I am running pymol on a MacPro with 16 Gb of RAM and running leopard. I searched over the internet but I could not find a 64-bit version for MacOSX. Is there a 64-bit macpymol available? If not is it possible to compile a 64-bit version? Many Thanks, Lucas -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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 -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] RMSD for ALL ATOMS against ALL ATOMS
Hi Renuka,
With a little bit of Python programming and better understanding of
structure alignment in PyMOL you should be able to complete your task.
First, check out the structure alignment category on the PyMOLWiki (
http://www.pymolwiki.org/index.php/Category:Structure_Alignment). Read the
difference between fitting (eg. 'fit') and aligning (eg. 'align'). PyMOL
also comes with built-in help, so try help align to get help and details
on the 'align' command. For pairwise aligning check out the alignto
command on the cealign webpage in the PyMOLWiki--this will show you how to
iterate over loaded proteins and align them to one target.
Here's some code to start with:
#start Python in PyMOL
python
# get the list of objects
p = cmd.get_names(objects)
# create the dictionary of results
results = {}
for curO in p:
if curO not in results: results[curO] = {}
for curI in p:
results[curO][curI] = cmd.align(curO, curI, cycles=0)
import pprint
pprint.pprint(results)
# stop python in PyMOL
python end
Cheers,
-- Jason
On Wed, Apr 14, 2010 at 11:29 AM, Renuka Robert renukarob...@ymail.comwrote:
Hi All Pymol users
I have a set of 40 X-ray crystallographic structures complexed with
inhibitors belonging to a specific family of kinases. Binding site residues
within 5 angstrom from the inhibitor were selected for each PDB structure
and saved separately. Now i have a set of 40 PDB files which has only the
binding site residues.
I want to perform RMSD for ALL ATOMS against ALL ATOMS. The first
structure should be fixed and compared with the remaining 39 structures. For
the next time, second structure is fixed and so on for all the 40
structures. Literally it should look like a 40X40 matrix table.
I used align, fit and rms commands. Each one gives different values.
Which is the best? Can you help me?
Thank you in advance
Renuka
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
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___
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--
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PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
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Re: [PyMOL] Res: Pymol 64-bits MacOSX
Lucas, If you'd like, please send me your session file and I can take a look at ray tracing it or making it possible for you to ray trace it. I did a small study a few years ago and found that if you can hide/remove atoms for PyMOL that won't make a difference in the scene, that could help you out. If you don't want to mess with it, feel free to send me the session file and I'll take a look. Last, try help faster in PyMOL for some more hints. -- Jason On Wed, Apr 14, 2010 at 2:16 PM, Lucas Santos lusasan...@yahoo.com.br wrote: Hi Jason, Sorry for taking that long to answer you, I was out of town. Well the picture that I have has 1441X814 pixels, which is way below your 4000X4000 pixels. I don't believe the resolution is the issue here but the complexity of the scene - I am trying to ray four big proteins (the complex formed by them is around 200kd) and a short stretch of DNA (40bp). Furthermore, I just don't want to ray only the cartoon, but the the cartoon together with the surface - pymol rays perfectly the cartoon but when I add the surface it becomes memory-demanding. Thank you, Lucas - Mensagem original De: Jason Vertrees jason.vertr...@schrodinger.com Para: Lucas Santos lusasan...@yahoo.com.br Cc: pymol-users@lists.sourceforge.net Enviadas: Sexta-feira, 9 de Abril de 2010 17:29:24 Assunto: Re: [PyMOL] Res: Pymol 64-bits MacOSX Lucas, How many pixels in your image? Also, how complex are your scenes? I've managed to pump out images at 4000x4000 (16,000,000 pixels). We can probably go larger, with some effort. What resolutions and complexities have others managed? Cheers, -- Jason On Fri, Apr 9, 2010 at 2:45 PM, Lucas Santos lusasan...@yahoo.com.br wrote: Hi, I tried to change the hash_max but it still crashing, I guess the images are quite big. Anyway, I will try to install PyMol under snow leopard (I got the disk but haven't installed yet). Thank you all for the help! Cheers, Lucas - Mensagem original De: Jason Vertrees jason.vertr...@schrodinger.com Para: Lucas Santos lusasan...@yahoo.com.br Cc: pymol-users@lists.sourceforge.net Enviadas: Sexta-feira, 9 de Abril de 2010 11:45:23 Assunto: Re: [PyMOL] Pymol 64-bits MacOSX Lucas, Try reducing your hash_max setting (http://www.pymolwiki.org/index.php/Hash_max). This will may ray tracing slower, but allows for larger images. Also, 64-bit MacPyMOL does not yet exist; we're still waiting on Tcl/Tk to update to 64-bit Carbon/Cocoa as they're using 32-bit now which is what our Pmw is built against. Cheers, -- Jason On Fri, Apr 9, 2010 at 11:22 AM, Lucas Santos lusasan...@yahoo.com.br wrote: Hi there, I have been facing some memory problems with macpymol 32-bits lately. When I try to ray a couple of big images my pymol crashes (malloc error), issue that could be easily fixed just by using a 64-bit pymol version - physical memory is not an issue I am running pymol on a MacPro with 16 Gb of RAM and running leopard. I searched over the internet but I could not find a 64-bit version for MacOSX. Is there a 64-bit macpymol available? If not is it possible to compile a 64-bit version? Many Thanks, Lucas -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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 -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed
Re: [PyMOL] RMSD for ALL ATOMS against ALL ATOMS
rms and fit gave you different values? They have never given me different
values.
Example:
from pymol import cmd
cmd.fetch('1nmr')
cmd.split_states('1nmr')
for i in xrange(1,21):
for j in xrange(1,21):
prot_i = '1nmr_%04d' %i
prot_j = '1nmr_%04d' %j
rms_val = cmd.rms(prot_i, prot_j)
fit_val = cmd.fit(prot_i, prot_j)
print rms_val-fit_val
prints 400 lines of 0.0
-David
On Wed, Apr 14, 2010 at 11:29 AM, Renuka Robert renukarob...@ymail.comwrote:
Hi All Pymol users
I have a set of 40 X-ray crystallographic structures complexed with
inhibitors belonging to a specific family of kinases. Binding site residues
within 5 angstrom from the inhibitor were selected for each PDB structure
and saved separately. Now i have a set of 40 PDB files which has only the
binding site residues.
I want to perform RMSD for ALL ATOMS against ALL ATOMS. The first
structure should be fixed and compared with the remaining 39 structures. For
the next time, second structure is fixed and so on for all the 40
structures. Literally it should look like a 40X40 matrix table.
I used align, fit and rms commands. Each one gives different values.
Which is the best? Can you help me?
Thank you in advance
Renuka
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
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--
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Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
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