Re: [PyMOL] writing out the surface
I finally got back to this, and I'm still having some trouble. The surface
I write out seems to be offset from what I'm viewing in PyMOL. I define the
following functions:
def getIndexedFaceSet(wrlname):
f = file(wrlname)
for line in f:
if 'geometry IndexedFaceSet {' in line:
break
else:
print Could not find IndexedFaceSet
return None
assert 'coord Coordinate' in f.next()
assert 'point' in f.next()
points = []
for line in f:
if not line.strip(): continue
line = line.strip()
if ']' in line:
break
if line.endswith(','):
line = line[:-1]
points.append(','.join(line.split()) + '\n')
return points
def pts2pdb(ptsname,pdbname):
f = file(pdbname,'w')
atomid,resi = 1,1
for line in open(ptsname):
line = line.strip()
if not line: continue
c = [float(x) for x in line.split(',')]
f.write('ATOM %06s %4s PHO %04s
%8.3f%8.3f%8.3f\n'%(atomid,resi,'C',c[0],c[1],c[2]))
atomid += 1
f.close()
def
writeSurfaceValue(objname,wrlname='/tmp/tmp.wrl',ptsname='/tmp/tmp.pts',pdbname='/tmp/tmp.pdb'):
cmd.hide('everything')
cmd.show('surface',objname)
cmd.save(wrlname)
points = getIndexedFaceSet(wrlname)
f = file(ptsname,'w')
f.writelines(points)
f.close()
pts2pdb(ptsname,pdbname)
cmd.extend('write_surface_value',writeSurfaceValue)
and then do
fetch 1rx1
set surface_solvent, 1
show surface
run whatever file defines the above functions
write_surface_value 1rx1
load /tmp/tmp.pdb
show spheres, tmp
and the tmp object looks like it has the right shape, but is clearly offset
from 1rx1.
I have a feeling I'm doing something simple and obvious wrong, but I'm not
sure what.
Thanks,
-Michael
On Mon, Jun 11, 2012 at 10:47 PM, Michael Lerner mgler...@gmail.com wrote:
Hi all,
Tsjerk- Thanks. I'm not sure how I missed that, given that it's even
mentioned on the wiki on the surface page under the clear heading
Exporting Surface/Mesh Coordinates to File :-|. (
http://www.pymolwiki.org/index.php/Surface#Exporting_Surface.2FMesh_Coordinates_to_File).
I don't know anything about VRML, but I found some documentation online at
http://www.c3.hu/cryptogram/vrmltut/part5.html and it looks really
straightforward. The surface will show up in the VRML file as an
IndexedFaceSet, and the points are just XYZ triples, and I can safely
ignore everything else.
Darrell- Thanks. I'll build that in as an option.
Takanori- Thanks. That's really cool. I happen to want solvent accessible
surfaces rather than isosurfaces, but dump is definitely going into my
bag of tricks.
Cheers,
-Michael
On Mon, Jun 11, 2012 at 8:57 PM, Takanori Nakane
t.nak...@mail.mfour.med.kyoto-u.ac.jp wrote:
Hi,
Another way:
There is an undocumented API called 'dump', which can
dump coordinates of isomesh/isosurface to a file.
For mesh, it dumps a list of vertex coordinates, which
can be rendered as GL_LINE_STRIP.
For surface, it dumps a list of pairs of a vertex coordinate
and its vertex normal vector, which can be rendered as GL_TRIANGLES.
Please examine my old post for a script example.
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10012.html
Best regards,
Takanori Nakane
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Earlham College - Drawer 111
801 National Road West
Richmond, IN 47374-4095
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[PyMOL] 3D printing question
Hi all, I just got a MakerBot Replicator, and I'd obviously like to try my hand at printing 3D models from PyMOL. If anybody else is doing such things, are there any recommendations for the most straightforward way to go from PyMOL to something that repg can read? A lot of the software I'm trying to use as intermediates between the two is proving to be troublesome. Cheers, -Michael -- Michael Lerner Department of Physics and Astronomy Earlham College - Drawer 111 801 National Road West Richmond, IN 47374-4095 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ 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] writing out the surface
Hi all, If I have a surface representation, is there currently a way to write it out as points (perhaps with a desired spacing) to a file? I know that the answer used to be no, but I thought I'd check just in case there was a new function that I didn't know about. Cheers, -Michael -- Michael Lerner Department of Physics and Astronomy Earlham College - Drawer 111 801 National Road West Richmond, IN 47374-4095 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ 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] writing out the surface
Hi all, Tsjerk- Thanks. I'm not sure how I missed that, given that it's even mentioned on the wiki on the surface page under the clear heading Exporting Surface/Mesh Coordinates to File :-|. ( http://www.pymolwiki.org/index.php/Surface#Exporting_Surface.2FMesh_Coordinates_to_File). I don't know anything about VRML, but I found some documentation online at http://www.c3.hu/cryptogram/vrmltut/part5.html and it looks really straightforward. The surface will show up in the VRML file as an IndexedFaceSet, and the points are just XYZ triples, and I can safely ignore everything else. Darrell- Thanks. I'll build that in as an option. Takanori- Thanks. That's really cool. I happen to want solvent accessible surfaces rather than isosurfaces, but dump is definitely going into my bag of tricks. Cheers, -Michael On Mon, Jun 11, 2012 at 8:57 PM, Takanori Nakane t.nak...@mail.mfour.med.kyoto-u.ac.jp wrote: Hi, Another way: There is an undocumented API called 'dump', which can dump coordinates of isomesh/isosurface to a file. For mesh, it dumps a list of vertex coordinates, which can be rendered as GL_LINE_STRIP. For surface, it dumps a list of pairs of a vertex coordinate and its vertex normal vector, which can be rendered as GL_TRIANGLES. Please examine my old post for a script example. http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10012.html Best regards, Takanori Nakane -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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 Department of Physics and Astronomy Earlham College - Drawer 111 801 National Road West Richmond, IN 47374-4095 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ 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] Electrostatic calculations with ligand bound
Hi Andrew, The main limitation for problems like this is that you need to have parameters for the ligand. Making sure that you have good parameters is often an expert-level topic, and you're probably best served by the APBS or PDB2PQR listservs as well as the literature ... but, you can get a decent start on things with PDB2PQR itself. See http://www.poissonboltzmann.org/pdb2pqr/examples/ligand-parameterization for some good starting instructions. Once you have a PQR file that includes both the protein and the ligand, the PyMOL/APBS plugin should do everything that you need. If that doesn't solve your problem, please let me know. Cheers, -Michael On Tue, Nov 29, 2011 at 11:44 AM, Malaby, Andrew andrew.mal...@umassmed.edu wrote: Hey guys, I am trying to calculate electrostatics with a ligand bound to my molecule using ABPS. I am not having success. Everything I've read seems to say that this is a normal limitation with APBS, and I've tried other programs to no avail. I have not been able to rebuild my molecule in the correct format either. Any help here is greatly appreciated. Andrew UMass Med School, Worcester, MA -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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 Department of Physics and Astronomy Earlham College - Drawer 111 801 National Road West Richmond, IN 47374-4095 -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ 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 pymol 1.4.1 source to windows. Easy.
Hi. I was very happy to find a post how to easy install pymol 1.4 from source on windows. 1) Install python, 2.5, or 2.6 or 2.7 for windows. 2) Download appropriate installer from: http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol Select according to your python version. 3) Run it 4) PyMOL is now installed in: C:\Python2X\PyMOL A) C:\Python2X\PyMOL\PDB_file.reg should be edited in a text editor, to match your python version. Run it. B) Pymol is started by clicking C:\Python27\PyMOL\pymol.cmd which executes python on C:\Python27\PyMOL\pymol-launch.py Happy pymoling. Best Troels -- EMC VNX: the world's simplest storage, starting under $10K The only unified storage solution that offers unified management Up to 160% more powerful than alternatives and 25% more efficient. Guaranteed. http://p.sf.net/sfu/emc-vnx-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) -- EMC VNX: the world's simplest storage, starting under $10K The only unified storage solution that offers unified management Up to 160% more powerful than alternatives and 25% more efficient. Guaranteed. http://p.sf.net/sfu/emc-vnx-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] loading gro files
...@schrodinger.com (o) +1 (603) 374-7120 -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 ___ 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 ___ 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 Department of Physics and Astronomy Earlham College - Drawer 111 801 National Road West Richmond, IN 47374-4095 -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2___ 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] How to manage plugin dependencies
Hi Osvaldo, What module? Newer versions of PyMOL ship with a much more featured set of Python modules (scipy, numpy, matplotlib, Bio, etc.). Cheers, -Michael On Sun, Jul 31, 2011 at 12:10 AM, Osvaldo Martin aloctavo...@gmail.comwrote: Hi Everyone, I`m writing a Python plug-in that depends on a certain Python module. For Linux users It would be easy to install this module because is available through the repositories (I think Mac OsX has a repositories system too, but I am not sure) . But for Windows this could be a little more complicated, 1) They don´t have a repository system and 2) Python is not installed by default in Windows, hence if they install any Python module this module will not be available to PyMol. I think there are at least two options. 1) The easy one (for me): To distribute a README file with the instructions to install the plugin in each platform and to make my plug-in to check if the module if available, if not ask the user to install it. 2) The easy one (for the user): To distribute this module with my plug-in, and create some installer to perform the installation in a more or less automatic way. Which option would be the better? It is option 2 to complicated to implement?, it is worthwhile? which are the easiest way to install Python modules on Windows and Mac OsX (and making them available to PyMol)? Thanks in advance. Cheers, Osvaldo. -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ 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) -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ 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 calculation sans alignment
PyMOL's rms_cur command will do what you want. E.g. fetch 1rx1 fetch 1ra1 # reports Executive: RMS = 34.329 (159 to 159 atoms) # because the structures still need to be translated and rotated rms_cur (1rx1 and name CA), (1ra1 and name CA) # reports Executive: RMS =0.862 (159 to 159 atoms) # because it calculates translated/rotated value, but does now # apply the translation/rotation to the molecules rms (1rx1 and name CA), (1ra1 and name CA) # reports Executive: RMS =0.391 (1026 to 1026 atoms) # standard PyMOL align, which also translates and rotates align 1rx1, 1ra1 # both of these report Executive: RMS =0.862 (159 to 159 atoms) # because the structures have now been translated and rotated rms_cur (1rx1 and name CA), (1ra1 and name CA) rms (1rx1 and name CA), (1ra1 and name CA) Cheers, -Michael On Fri, Jul 22, 2011 at 10:19 AM, Thomas Grant tgr...@hwi.buffalo.eduwrote: Dear all, I'm attempting to align a series of structures using the CEAlign plug-in in PyMOL due to a lack of any detectable sequence homology. CEAlign does a good job of aligning and the fits are very reasonable. However, the RMSD that is calculated is based only on the c-alphas that were actually aligned, not based on the total number of c-alphas in the structure. After searching online I have been unable to find any software or servers that will simply calculate the RMSD of two structures as is, without aligning them first. I would think this would be a relatively straightforward thing to do, just to calculate RMSD from two existing structures without translation or rotation for alignment. Does anyone know of a way either in PyMOL or in general to simply calculate the RMSD between all c-alphas of two structures? Obviously it won't necessarily be a one-to-one ratio of c-alphas, but I can manually curate the pdb to include only the equivalent and aligned residues, even if not used in the CEAlign algorithm, so that there are the same number of c-alphas in both structures. Thank you for any help and suggestions, Tom -- 10 Tips for Better Web Security Learn 10 ways to better secure your business today. Topics covered include: Web security, SSL, hacker attacks Denial of Service (DoS), private keys, security Microsoft Exchange, secure Instant Messaging, and much more. http://www.accelacomm.com/jaw/sfnl/114/51426210/ ___ 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) as of August 15th: Department of Physics and Astronomy Earlham College 801 National Road West Richmond, IN 47374-4095 -- 10 Tips for Better Web Security Learn 10 ways to better secure your business today. Topics covered include: Web security, SSL, hacker attacks Denial of Service (DoS), private keys, security Microsoft Exchange, secure Instant Messaging, and much more. http://www.accelacomm.com/jaw/sfnl/114/51426210/___ 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] ContactsNCONT script error
Hi Ivan, There's definitely a bug in that script. It looks like most of the file has one extra space of indentation. I don't feel comfortable changing it at the moment, as I'm not on a machine that has ccp4, but perhaps someone else can fix and test it. If not, I'll fix it tomorrow. Cheers, -Michael On Wed, May 25, 2011 at 7:35 PM, Campeotto, Ivan i.campeo...@imperial.ac.uk wrote: Dear All, I would like to compare the intermolecular crystal contacts in seven crystal forms of the same enzyme. I produced a list of contacts for each crystal form using the program NCONT from CCP4 and I found the ContactsNCONT script in the PyMOL Wiki ( http://www.pymolwiki.org/index.php/ContactsNCONT), which would save me a lot of time. Unfortunately, when I run the ContactsNCONT script, I always have the following message with different PCs running different OS (Windows, RedHat or Mac): File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py, line 338, in parse parsing.run_file(path,self.pymol_names,self.pymol_names) File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parsing.py, line 455, in run_file execfile(file,global_ns,local_ns) File C:/Documents and Settings/Ivan/Desktop/ContactsNCONT.py, line 3 def parseContacts( f ): ^ IndentationError: unexpected indent Any suggestion will be more than appreciated. Thank you in advance, Regards Ivan Campeotto Centre for Molecular Microbiology and Infection Imperial College London -- vRanger cuts backup time in half-while increasing security. With the market-leading solution for virtual backup and recovery, you get blazing-fast, flexible, and affordable data protection. Download your free trial now. http://p.sf.net/sfu/quest-d2dcopy1 ___ 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) -- vRanger cuts backup time in half-while increasing security. With the market-leading solution for virtual backup and recovery, you get blazing-fast, flexible, and affordable data protection. Download your free trial now. http://p.sf.net/sfu/quest-d2dcopy1___ 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] How to construct a view showing only a single contiguous cavity
The last time I tried to do something similar, I found HOLLOW ( http://hollow.sourceforge.net/) to be very useful. There's a nice tutorial for showing a binding site, rather than an interior cavity, here: http://hollow.sourceforge.net/binding.html . Cheers, -Michael On Fri, May 20, 2011 at 7:11 PM, Ben Roberts b...@roberts.geek.nz wrote: Hi list, I'm trying to use PyMOL to construct an image of the total contiguous contact surface that starts at a particular place on the surface of a protein, without all the visual distraction and clutter that comes from other regions of the protein surface (not to mention internal cavities). I started by rendering up the whole protein as Contact surface with Cavities and pockets only shown. Unfortunately, this displays a large number of bubbles, some of which, despite being far away in space from the region of interest, manage to effectively obscure bits and pieces of it. So my next thought was to try removing the extraneous bits, however, I can't seem to select atoms in surface view; I have to display everything as lines or similar. Removing things that way gets very unwieldy, not least because of all the atoms that don't contribute anything to the surface but appear in front of, behind, or otherwise near to the atoms that do so. A third option I tried was to build the surface up, starting from the known points of interest, but this too is painstaking because of the need to guess where I should next expand the selection to in order to fill in the gaps. A remaining method of getting only the cavity of interest would, I guess, be to create a selection consisting only of those atoms that contribute something to the currently rendered surface (in this case, cavities and voids). I could then render those as spheres or something and hide unwanted contributors. Is there a way of specifying such a selection? Alternatively, is there some other smart way to achieve what I want (and by smart, I mean a way that isn't time- consuming and unusually error-prone)? I've already tried Googling, to no avail; I got, mostly, instructions about how to display surfaces in general. I should mention that I'm using a recent version of MacPyMol, on Mac OS X 10.6.7. Any tips are welcome. Thanks! Best regards, Ben -- For greater security, I support S/MIME encryption. -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ 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) -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ 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] Fetching scripts
Hi Peter, On Wed, May 4, 2011 at 6:56 PM, Pete Meyer pame...@mcw.edu wrote: - Sandboxing would be ideal, but I don't know if there's infrastructure in python to support it. It might be easier to filter fetched scripts to only allow a restricted subset of python functions (the ast library looks like it might make this a bit easier). If a script can't access the network or hard disk, then it doesn't need to be trusted as much. There are a couple of issues with this - The last time I checked (which, admittedly, was a couple of years ago), many people had tried and failed to set up such an environment within Python. It turned out that there were very clever ways to get around any sort of reasonable restrictions that people tried to impose (i.e. a guaranteed-to-be-safe script couldn't actually do anything useful). I know there has been a lot of desire for this, so maybe the problem has been solved. - There are some plugins that need access to the hard disk. I'm not sure about scripts. If there exists a reasonable sandboxing (or AST-based) solution, we'll have to run those scripts in untrusted mode, which is probably fine. - The wiki doesn't appear to support SSL. So that means trusting the network to get to the wiki correctly, in addition to the wiki itself. I don't have any good ideas for how to work around this one. My guess is that there's just never been a real need for SSL. Jason would be the real authority here, but I'd guess that SSL would be possible if it there's a strong push for it. -Michael Pete Michael Lerner wrote: Hi all, I'm considering building in a mechanism for automatically fetching scripts from the PyMOL Wiki. The goal is to allow users to say fetch findSurfaceResidues, type=script findSurfaceResidues doShow=True, cutoff=0.5 The convenience benefits are obvious, especially for new users, and I think that lowering the barrier to script usage will greatly increase both the number of people who use various scripts and the incentive to place scripts on the wiki (especially if the fetch mechanism makes it easy for script authors to provide a citation/DOI/etc.). I've put up a tentative page about this on the wiki ( http://pymolwiki.org/index.php/Fetching_scripts), and I'd love comments either via the list, private email or on the wiki, especially about - whether you think it's a good idea - security and validation - options you'd like - implementation issues The plan is to write this as a userland script first. If issues relating to security and validation can be resolved, we'll see if the official builds want to include it. Cheers, -Michael -- 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) -- 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) -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ 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] APBS Plugin: protein out of grid
Can you send me the files (off list) so that I can take a look? Thanks, -Michael On Thu, May 5, 2011 at 5:11 PM, Ricardo O. S. Soares ross_...@yahoo.com.brwrote: Dear users, there's a particular case where I'm using the APBS plugin and the resultant grid leaves a portion of the protein out of it. This portion is show in full white because no potential is calculated there. Why isnt the grid centered as usual? Changing the values by hand and them recaulculating does not seem to change the grid at all. Thanks, Ricardo. -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ 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) -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ 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] Fetching scripts
Hi all, I'm considering building in a mechanism for automatically fetching scripts from the PyMOL Wiki. The goal is to allow users to say fetch findSurfaceResidues, type=script findSurfaceResidues doShow=True, cutoff=0.5 The convenience benefits are obvious, especially for new users, and I think that lowering the barrier to script usage will greatly increase both the number of people who use various scripts and the incentive to place scripts on the wiki (especially if the fetch mechanism makes it easy for script authors to provide a citation/DOI/etc.). I've put up a tentative page about this on the wiki ( http://pymolwiki.org/index.php/Fetching_scripts), and I'd love comments either via the list, private email or on the wiki, especially about - whether you think it's a good idea - security and validation - options you'd like - implementation issues The plan is to write this as a userland script first. If issues relating to security and validation can be resolved, we'll see if the official builds want to include it. Cheers, -Michael -- 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) -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ 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 Protein Dimension
Hi Martin,
The following works for me, although I needed to change 'protein' to
'polymer'. Is 'protein' normally supported as a selection? It doesn't seem
to be in 1.4.1.
from pymol import cmd
cmd.fetch('1rx1')
a = cmd.get_extent('polymer')
print a is,a
Hope that helps,
-Michael
On Tue, Apr 26, 2011 at 7:40 AM, Martin Hediger ma@bluewin.ch wrote:
Dear all
I found that PyMOL offer the cmd.get_extent('protein') function, which
returns the dimensions of the selection.
Is it complicated to make this function available from within an
ordinary Pythonscript?
Thanks for hints.
Martin
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Re: [PyMOL] Hiding individual dash/distance objects within a merged-dash object
Hi Harry, If they've been combined using the group command, you can ungroup them: fetch 1rx1 # make some distance objects dist measure01, 19/C, 20/C dist measure02, 20/C, 21/C dist measure03, 158/C, 159/C dist measure04, 157/C, 159/C # group them group g1, measure01 or measure02 group g2, measure03 or measure04 #ungroup all of them (this leaves empty groups, which you can delete if you'd like) ungroup measure* Hope that helps, -Michael On Tue, Apr 26, 2011 at 5:47 AM, Harry Jubb hj...@cam.ac.uk wrote: Hi Everyone, I'd like to ask for some help with dash/distance objects. I have PyMOL session files which show inter-molecular interactions using PyMOL distance objects. These were created using a script which colours each distance object and merges them according to type of interaction. The problem I'm having is that I would prefer to visualise the interactions on a per-residue basis, i.e. showing all the interactions for one or more residues but not the others, but as the dashes are merged by interaction type I can only hide by that category. Extensive Googling has not led me to a solution to select and hide individual dashes that are merged into one UI object, so I'd like to ask if it is possible to do this? I'm unfortunately no longer able to run the script again (I am at the end of a time limited project and am preparing figures) and I would prefer not to replace each dash manually. I hope this is clear, the crux of what I am asking is if it is possible to select and/or hide individual distance objects in a pymol session after they have been merged into one object. Un-merging them would also be an attractive solution. Thanks, Harry -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ 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) -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ 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] Hiding individual dash/distance objects within a merged-dash object
Hi Harry, As far as I know, this is not currently possible in PyMOL, but perhaps someone will correct me on this. -Michael On Tue, Apr 26, 2011 at 9:27 AM, Harry Jubb hj...@cam.ac.uk wrote: Hi Michael, Thank you for your response. The problem is that for types of inter-molecular interaction all of the visual distances are merged into one object in the sidebar (as if created using the measurement wizard with the merge with previous option on), for which unfortunately the ungroup command doesn't seem to work for. Left-clicking on the interaction type in the GUI sidebar toggles show/hide for every distance of that interaction type, and there are no further disclosure squares which indicates that the distances are grouped rather than merged. Ideally I'd like to be able to un-merge these objects to make each dash an object that I can hide or show individually so I can switch off the ones not connected to a residue of interest. Even better (if possible) would be to only show dashes connected to a residue of choice. I hope that makes sense. Thank you for your help, Harry On 26 Apr 2011, at 13:59, Michael Lerner wrote: Hi Harry, If they've been combined using the group command, you can ungroup them: fetch 1rx1 # make some distance objects dist measure01, 19/C, 20/C dist measure02, 20/C, 21/C dist measure03, 158/C, 159/C dist measure04, 157/C, 159/C # group them group g1, measure01 or measure02 group g2, measure03 or measure04 #ungroup all of them (this leaves empty groups, which you can delete if you'd like) ungroup measure* Hope that helps, -Michael On Tue, Apr 26, 2011 at 5:47 AM, Harry Jubb hj...@cam.ac.uk wrote: Hi Everyone, I'd like to ask for some help with dash/distance objects. I have PyMOL session files which show inter-molecular interactions using PyMOL distance objects. These were created using a script which colours each distance object and merges them according to type of interaction. The problem I'm having is that I would prefer to visualise the interactions on a per-residue basis, i.e. showing all the interactions for one or more residues but not the others, but as the dashes are merged by interaction type I can only hide by that category. Extensive Googling has not led me to a solution to select and hide individual dashes that are merged into one UI object, so I'd like to ask if it is possible to do this? I'm unfortunately no longer able to run the script again (I am at the end of a time limited project and am preparing figures) and I would prefer not to replace each dash manually. I hope this is clear, the crux of what I am asking is if it is possible to select and/or hide individual distance objects in a pymol session after they have been merged into one object. Un-merging them would also be an attractive solution. Thanks, Harry -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ 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) --- Harry Jubb Part II Biochemistry Homerton College UTN: 131 2726 M: 0790 813 4735 -- 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) -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ 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] Convert pml script to Pymol Python script
It's not elegant at all, but it's worth knowing that you can use cmd.do(...) as a quick fix for lines that aren't immediately easy to convert. Even a mostly-working pml2py tool would be a useful addition to the wiki. Cheers, -Michael On Fri, Apr 8, 2011 at 2:09 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Matthias, There is no script that I'm aware of, but writing one should be rather straightforward because of how the API is organized: commandName arg1, arg2, arg3 becomes cmd.commandName(arg1, arg2, arg3) The hardest part would be determining when to quote strings versus not quoting numbers and variables. You might be able to reflect against the API for a more robust script (http://diveintopython.org/power_of_introspection/index.html). Java's great at that, not sure about Python. Good luck. Cheers, -- Jason On Fri, Apr 8, 2011 at 1:01 PM, Matthias Schmidt matthias.rene.schm...@gmail.com wrote: Hi, I have a few pml scripts for pymol that I would like to rewrite properly in python, making use of Pymol's ability to interprete Python scripts. Do you know of an interpreter that converts pml scripts automatically to python scripts for Pymol? Since the number of tasks that you can do in pml is finite, this should be possible, or not? Best, Matthias -- Structural Bioinformatics and Computational Biochemistry Unit Dept. of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU U.K. Telephone: 01865 613304 Fax: 01865 613238 -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ 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 -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ 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) -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev___ 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] How to save APBS-generated maps
Hi Cale, After you run the APBS calculation, you will find the relevant files stored in a temporary directory. The default location of that directory depends on your operating system and system configuration, but you can set it explicitly in the Plugin's Temp File Locations tab. The name of the file containing the map is pymol-generated.dx by default, although you can change both the name and the location on that tab. Cheers, -Michael On Fri, Apr 1, 2011 at 12:49 PM, Cale Dakwar c.dak...@gmail.com wrote: Hello all, Is there a quick way to save an APBS PyMol Plugin generated map from within pymol? Thanks in advance, Cale -- Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf ___ 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) -- Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf ___ 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] How to get pymol 1.4
@lists.sourceforge.net http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar http://p.sf.net/sfu/intel-dev2devmar ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ 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) -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar___ 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] Adding Hydrogens
I've had good results with MolProbity ( http://molprobity.biochem.duke.edu/index.php?MolProbSID=6b810d461879ca495f8d7898629dc18ceventID=15) in the past. I had a script that would let me cycle through all of the HIS residues, add hydrogens, and cycle between states. It's broken at the moment. The trick was that PyMOL doesn't care about the name of the residue, so you have to manually cycle the valences. On Wed, Mar 16, 2011 at 11:22 AM, Martin Hediger ma@bluewin.ch wrote: Dear All I would like to ask if the PyMOL function to add hydrogens to an entire protein also has options, meaning is it possible to set the protonation state of individual residues specifically? Like in a list or something? h_add, His202:+1 or so? And, it can be relevant at what atom a residue gets protonated: His can be protonated at Nd, or Ne or both. Is there a way to control this? On a more general note: what other smart hydrogen adding tools are there out there anyway? Does anyone know a really smart tool for this? I know OpenBabel has a pH parameter. But on the other hand OpenBabel just appends the hydrogens to the PDB file, whereas PyMOL really writes them within the block of atoms corresponding to one residue. Also, AutoDock can add hydrogens and it even has an option for the protonation state of histidine, but it doesn't seem to work in my case. Thanks for your answers and input. martin -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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) -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ 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] movie with morph and electrostatics
If you know a bit of python, you can make a version of the Plugin that will
do this via repeated calls to self.execute('Run APBS',refocus=False).
If this would be a generally useful feature, I could add a movie button to
the plugin so that it would step through all available frames, saving PNGs
for each.
Let me know,
-Michael
On Tue, Mar 15, 2011 at 1:13 PM, Ian Slaymaker slaym...@usc.edu wrote:
I am trying to figure out how to design a movie that will preform a morph
between two conformations of a protein, while having each chain move as a
rigid body, and recalculate the electrostatic surface for each midstate
between conformations. Can anyone offer me some suggestions on how to do
this?
Thank you!
Ian Slaymaker
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Re: [PyMOL] R: Re: plugin dependencies
I really like the fact that Jason will be including more libraries with PyMOL in the future. I once needed to distribute a library that depended on BioPython. It turned out that, in my case, I only cared about a few specific files from BioPython, so I was able to strip out the necessary functionality and just ship that with my plugin. I don't know exactly what you're doing, but that might be an option. Cheers, -Michael On Thu, Mar 10, 2011 at 9:25 PM, rv...@libero.it rv...@libero.it wrote: Hi Hongbo, thanks for your reply. So, how about ship all the BioPython packages you need in your python code together with your plugin? Of course all dependencies should be included. Is not so simple. A library like Biopython can't be installed as a plugin. An installer (OS specific) program is needed: the official windows installer I checked doesn't allow the user to choose the folder (this way the interpreter) where to install. Installing manually is still tricky for a not experienced user. Cheers, roberto Messaggio originale Da: hongbo@biotec.tu-dresden.de Data: 10/03/2011 12.57 A: pymol-users@lists.sourceforge.net Ogg: Re: [PyMOL] plugin dependencies Just another reminder: If the version of the external python and the python shipped with PyMOL are different enough on the user's computer, the package might still fail to work in PyMOL even if the user has installed the package using the external python and edited the PYTHONPATH. So, how about ship all the BioPython packages you need in your python code together with your plugin? Of course all dependencies should be included. On 03/10/2011 06:17 AM, rv...@libero.it wrote: Hello everyone, my plugin needs Biopython. I wish check the Biopython installation by try: from Bio import AlignIO # or similar except ImportError: .. prompt the user with a msg .. The problem is: what the msg to the user? Downloading and installing Biopython is not enough: If the user downloads and installs Biopython in the external python interpreter still Biopython continues to be unavailable for the internal python interpreter in pyMOL. Of course the user could edit the PYTHONPATH environment variable and so all the python interpreters can read Biopython but working with environment variables could be too difficult for a not experienced user. Is there a simpler way? Cheers, roberto -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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 -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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 -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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) -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ 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
Re: [PyMOL] Color scale changed in APBS?
Hi all, On Tue, Feb 22, 2011 at 8:00 AM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: Hi Wataru, in addition to what Jason mentioned: Have you tried to look at the potential mapped on the solvent accessible surface and display the molecular surface? If you display the potential like this the colors will be much more muted, on the other hand this is the setting you will find most often displayed in the literature. I think this is likely the case. Due to a lot of feedback, the plugin defaults changed to showing the solvent accessible surface a while ago (see the checkboxes in the Molecular Surface section of the Visualization panel). Another option is to have a look at the charge distribution of your molecule in the actual PQR file. The potential distribution is dependent on the charging algorithm used. I would recommend using/looking into PDQ2PQR, which is available from the APBS website and compare this to the homegrown charging algorithm from PyMol or GRASP for that matter. Many (most?) users of the plugin do indeed use PDB2PQR. It's worth noting that the current version of the plugin allows you to specify command line arguments to PDB2PQR (e.g. --ff=AMBER, etc. if you're interested in trying out different force fields). Cheers, -Michael Hope I did not muddle the water too much Carsten -Original Message- From: Wataru Kagawa [mailto:wkag...@aoni.waseda.jp] Sent: Monday, February 21, 2011 10:04 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Color scale changed in APBS? Dear PyMOL users: I recently used the APBS plugin (v1.3) to display the surface potential of a protein. I noticed that the charged surfaces were much more lightly colored, compared with the surface colors I have calculated in the past (maybe a year ago?) on the same protein, using the same softwares. The default settings and the same range (-10 kT to 10 kT) were used in both cases. Has anyone experienced this? I would appreciate any help. Wataru --- --- Index, Search Analyze Logs and other IT data in Real-Time with Splunk Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. Free Software Download: http://p.sf.net/sfu/splunk-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 -- Index, Search Analyze Logs and other IT data in Real-Time with Splunk Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. Free Software Download: http://p.sf.net/sfu/splunk-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) -- Index, Search Analyze Logs and other IT data in Real-Time with Splunk Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. Free Software Download: http://p.sf.net/sfu/splunk-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] Visualizing two surfaces using APB2tools2.1
Thanks for the nice writeup, Jason! There are two main ways that I know of to visualize two potentials at once. This is one. If you're looking at, e.g., a protein-protein interface, it may be useful to map two different electrostatic potentials to two different PyMOL objects. Here's my overly-cautious recipe for doing that: 1. Load up PyMOL with one of your structures. 2. Fire up the plugin. Click on Choose Externally Generated PQR File and point it at your PQR file. 3. Click on the Temp File Locations tab and change the name of the temporary DX file to something meaningful, e.g. structure1.dx 4. Set grid and Run APBS as normal. 5. Close the plugin. 6. Type delete all 7. Load up the second structure. 8. Repeat steps 2-4, changing the name to something like structure2.dx this time. Now you have two correctly generated electrostatics potential maps (note: the reason I had you do things with one structure at a time loaded in PyMOL is so that you wouldn't have to fiddle around with the Selection to use section of the Main options tab). Use the load command to load up the other pqr file and the other dx map, then use the visualization panes as normal. Cheers, -Michael On Tue, Feb 1, 2011 at 9:48 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Yarrow, Does anyone know how to visualize the surface potentials of two molecules simoutaneously using the APBS Tools2.1 plugin? Thanks. As Michael wrote the APBS plugin, he might have more to offer, but here's how I'd do it. I used this technique to look at two similar proteins side-by-side in PyMOL (see the 2nd image on http://www.pymolwiki.org/index.php/APBS). The trick is to (1) use grid_mode and grid_slots; and (2) rename the maps as appropriate. It's not hard, but will take a couple minutes. Here's how: # get two proteins; use whatever you like fetch 1rx1 1rx2, async=0 # put them in the same frame of reference for grid mode align 1rx1, 1rx2 # run APBS on protein #1, 1rx1 Plugin APBS Tools2 ... Under selection to use type (polymer) and 1rx1 # rename the map set_name pymol-generated, 1rx1_map # run APBS on protein 2, 1rx2; remove the waters Plugin APBS Tools2 Under selection to use type (polymer) and 1rx2 # rename the map set_name pymol-generated, 1rx2_map # Now, using APBS show the surfaces make sure you choose # 1rx1_map for 1rx1 and 1rx2_map for 1rx2; click Update if those # map names are not present. ... # turn on grid mode set grid_mode # assign grid slots just to be sure the right maps # and proteins are in the right places set grid_slot, 1, 1rx1 set grid_slot, 1, 1rx1_map set grid_slot, 1, e_lvl_0_1 set grid_slot, 2, 1rx2 set grid_slot, 2, 1rx2_map set grid_slot, 2, e_lvl_1_1 Now, you should be set and have an image like that I posted on the PyMOLWiki. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ 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) -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d___ 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] APBS surface data export
Hi Matt, PyMOL does not currently allow you to export the data mapped to the surface. However, the dx format is very straightforward. It follows a subset of the OpenDX standard, as described on the APBS site ( http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/opendx-scalar-data ). I don't know much about surface file formats, but the PyMOL wiki mentions ( http://www.pymolwiki.org/index.php/Surface#Exporting_Surface.2FMesh_Coordinates_to_File) that you can save surface coordinates to a file. It might be possible for a developer (you?) to convince PyMOL to write out the electrostatic potential along with whatever else it's writing to the .wrl file. Hope that helps, -Michael On Mon, Jan 31, 2011 at 7:03 PM, Matteo Pendleton znfin...@gmail.comwrote: Greetings, I'm looking to use an electrostatic surface map for downstream calculations and was wondering whether it's currently possible (after using APBSv2 to calculate a surface potential map) to export a mesh of data points in a list format with each data point's associated potential? If not, does anyone have an outline of the file layout for the pymol-generated.dx file so I could write my own script to do it? Thank you kindly, Matt Pendleton Independent Researcher New York, NY -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ 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) -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d___ 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] Wiki down?
There's been a flood of spam to the wiki recently. Most of it has been obvious spammy pages, but someone also deleted the main page. Cute. On Thu, Jan 27, 2011 at 12:54 PM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: I am just getting a blank page when I try to access the Pymol Wiki. Do other people see the same problem? Carsten -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ 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) -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d___ 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] OpenDX files from opendx.org
Hi David, As far as I know, PyMOL is still using its own DX reading functions (primarily ObjectMapDXStrToMap in layer2/ObjectMap.c if anyone's curious). I don't think it would be too much work to get PyMOL to read regular.dx. As far as I can tell, the only problem is that PyMOL is expecting the line that starts with object 3 to say object 3 class array type double instead of object 3 class array float. As for regularskewed.dx, PyMOL *does* support non-orthogonal maps (see e.g. http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05870.html), but I'm not sure that PyMOL's DX reader supports them directly. I have not looked into the VMD plugins. If they support non-orthogonal DX maps out of the box, that might be a quick and easy solution. Cheers, -Michael On Fri, Oct 15, 2010 at 5:51 PM, David Hall li...@cowsandmilk.net wrote: I have long been happy reading .dx files produced by apbs and my own programs into pymol. Everything works great. Interestingly, when I save a .dx file from OpenDX (http://opendx.org), pymol seems to not be able to read it. I've attached two files that come from OpenDX's samples directory where loading into pymol gives the error ObjectMap-Error: Error reading map. Any help in what's wrong with these files (or how to patch the VMD plugins that I believe pymol uses to read in dx files) would be appreciated. -David -- Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-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) -- Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-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] Deleting and Loading multiple SDF files
Hi Renuka,
Please keep all PyMOL-related correspondence on the mailing list. That way,
other people can find the answers by reading the mailing list or searching
the web.
Your task is now getting a little more complicated. I think you'll probably
want to define some Python functions and use them. It's useful to know that
using the distance command with mode=2 will show polar contacts. Also,
distance objects with names starting with an underscore won't show up in the
GUI.
I'd do something like this:
1. Define some functions in a Python file that you can use via run (or
perhaps in your .pymolrc). [see
http://www.pymolwiki.org/index.php/Python_Integration and
http://www.pymolwiki.org/index.php/Script_Tutorial]. You'll need to pass the
name of your protein to these functions.
import os
from pymol import cmd
def loadclust(filename,protname):
cmd.load(filename)
dir,fname = os.path.split(filename)
# PyMOL automatically names the object by the filename
fname,extension = os.path.splitext(fname)
# cluster_4 -- 4
custernum = fname.split('_')[1]
# hidden from GUI display because it starts with _
polarname = '_polar_'+clusternum
cmd.dist(polarname,fname,protname,mode=2)
cmd.extend('loadclust',loadclust)
def delclust(filename):
dir,fname = os.path.split(filename)
# PyMOL automatically names the object by the filename
fname,extension = os.path.splitext(fname)
# cluster_4 -- 4
custernum = fname.split('_')[1]
# hidden from GUI display because it starts with _
polarname = '_polar_'+clusternum
cmd.delete(fname)
cmd.delete(polarname)
cmd.extend('delclust',delclust)
2. Then you should be able to use a similar procedure to
before. Remember that you now need to delete things and pass the name of
your protein to the functions so that polar contacts can be displayed
correctly:
for i in glob.glob(Model_1/cluster_*.sdf): loadclust(i,myprotein)
analyze things
for i in glob.glob(Model_1/cluster_*.sdf): delclust(i,myprotein)
for i in glob.glob(Model_2/cluster_*.sdf): loadclust(i,myprotein)
Unfortunately, I don't have any SD files on hand, so I haven't tested these!
Some modification may be necessary. You should also check out the script
that Jason linked.
Cheers,
-Michael
On Wed, Sep 22, 2010 at 11:52 AM, Renuka Robert renukarob...@ymail.comwrote:
Dear Michael
Thanks for your detailed reply. This is what exactly i needed. Now i want
to find the hydrogen bonding between each cluster files and the protein. So
i do the following step
cd /home/user
import glob
then I load the Model_1 files with
for i in glob.glob(Model_1/cluster_*.sdf): cmd.load(i)
Now hydrogen bond should be displayed between protein and
Model_1/cluster_*.sdf. Polar contacts in different colors would be more
appreciated.
Could you please attach your script in the above command, so that all the
cluster_*.sdf is loaded and its polar contacts is displayed in one press.
Thanks in advance
Renuka.
--- On *Wed, 22/9/10, Michael Lerner
mglerner+sourcefo...@gmail.commglerner%2bsourcefo...@gmail.com
* wrote:
From: Michael Lerner
mglerner+sourcefo...@gmail.commglerner%2bsourcefo...@gmail.com
Subject: Re: [PyMOL] Deleting and Loading multiple SDF files
To: Renuka Robert renukarob...@ymail.com
Cc: PyMOL-users@lists.sourceforge.net
Date: Wednesday, 22 September, 2010, 1:46 PM
Hi Renuka,
If I understand correctly, this is what you want to do:
1. Load up all of the cluster*.sdf files in Model_1.
2. Analyze them
3. Delete them
4. Load up all of the cluster*.sdf files in Model_2.
5. Analyze them
6. Delete them
etc.
If that's right, I think the easiest thing is just to change to the
directory that contains your Model_N subdirectories. In your example, that
would be:
cd /home/user
import glob
then load the Model_1 files with
for i in glob.glob(Model_1/cluster_*.sdf): cmd.load(i)
then analyze them. It sounds like you're analyzing them by hand; if you're
analyzing them by running some scripts, we can probably help to automate
that process as well.
After analyzing them, (and saving your results!), you'll want to delete the
current batch of cluster files and load the new ones:
delete cluster_*
for i in glob.glob(Model_2/cluster_*.sdf): cmd.load(i)
Note that you only have to type import glob once.
Hope that helps,
-Michael
On Wed, Sep 22, 2010 at 9:12 AM, Renuka Robert
renukarob...@ymail.comhttp://mc/compose?to=renukarob...@ymail.com
wrote:
Dear Pymol users
I have to do TWO jobs simultaneously in PYMOL.
JOB 1: Load multiple *sdf files
I have set of ligand files in *.sdf format as follows:
/home/user/Model_1/cluster_1.sdf
/home/user/Model_1/cluster_2.sdf
/home/user/Model_1/cluster_3.sdf
/home/user/Model_2/cluster_1.sdf
/home/user/Model_2/cluster_2.sdf
/home/user/Model_2/cluster_3.sdf
/home/user/Model_3/cluster_1.sdf
/home/user/Model_3/cluster_2.sdf
/home/user/Model_3/cluster_3
Re: [PyMOL] Wizard Measurement
Hi Martin,
I find that the easiest way to recreate things like this is with cmd.do.
cmd.do('wizard measurement') is identical to typing 'wizard measurement'
from the command line.
In this particular case, it looks to me like just calling
cmd.wizard('measurement') works. Did you find problems when you didn't call
refresh_wizard?
Thanks,
-Michael
On Sat, Sep 4, 2010 at 12:40 PM, Martin Hediger ma@bluewin.ch wrote:
Dear All
I'm trying to write a littel function that allows for a short cut to
invoke the wizard measurement. The idea is, that instead of having to
open the GUI menueMeasurement or typing wizard measurement, I would
like to be able to just type mes and have the measurement tool-box
available.
Observing what happens in the log-file when doing this shows that two
things happen:
wizard measurement
refresh_wizard
I figured out, that I can write cmd.wizard(measurement) into the
function definition (called mes, in mes.py), and the measurement box
appears. What I cant figure out is how to implement the refreshment of
the wizard using the PyMOL-API.
Can someone point this out to me?
Thanks for any help on this, btw. the same thing would kind of be nice
for mutagenesis.
Martin
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Re: [PyMOL] Start PyMOL from command line
Hi Martin, I know a few ways to do this: 1) If you've set your Mac up to load PDB files with PyMOL by default, you can just type open *.pdb from the command line. 2) Instead of using OS X's open command, you can launch PyMOL directly via /Applications/PyMOLX11Hybrid.app/Contents/MacOS/MacPyMOL *.pdb (you may have to change that depending on where you have PyMOL installed). 3) From within PyMOL, you can type from glob import glob for f in glob.glob(*.pdb): cmd.load(f) and it will load them all. There's more information to be found on the wiki ( http://www.pymolwiki.org/index.php/Launching_PyMOL), including information on how to set up aliases so that you can just type pymol to launch it. It's worth noting that pymol -c will launch PyMOL in batch mode without the GUI, which may not be what you want. Cheers, -Michael On Wed, Sep 1, 2010 at 9:44 AM, Martin Hediger ma@bluewin.ch wrote: Dear All I'm using Mac OS X and would like to start PyMOL from the command line, so I can open up .pdb files from a command line argument by issuing $ pymol -c /directory/*pdb (for some reason, within pymol it seems to be not possible to issue 'PyMOL *pdb'). When I enter 'pymol' in the Terminal, the Shell freezes and I have to kill the process. What is required to do so PyMOL becomes launchable from the command line. Thanks for suggestions. Martin -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd ___ 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) -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd___ 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 and APBS
Hi, Which version of PyMOL, APBS and PDB2PQR are you using? If you send me a PQR file off-list, I can take a closer look at what's going on. Thanks, -Michael On Thu, Apr 15, 2010 at 12:01 AM, J. Fleming moloch...@gmail.com wrote: Hi all, I've been trying to get APBS Tools and/or APBSTools2 running for a few weeks now on multiple linux systems (RedHat and Fedora). I've Installed MALOC and APBS Tools. I can start up Pymol through Phenix, load a .pqr generated from a PDB2PQR server, start APBS Tools, set the grid, but when I click on Run APBS I get: ObjectMapLoadDXFile-Error: Unable to open file! If I use the pymol generated PQR option with my .pqr even though it is a PDB2PQR server generated file APBS runs and states X atoms did not have properties assigned and to either remove or fix the atoms. How can I fix them? The problem residues are just regular amino acids; no split confrimations etc. I've also tried editing out the PDBs chain name before converting to the PDB to PQR but that didn't work. Another things I've tried is using APBSTools 2 but it errors as soon as I click set grid with: Error: 2 ... Attribute Error: elec_radius. I really need to get this to work but I have no clue what to try next. Thanks in advance for any thoughts. -Jon -- 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 -- 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) -- 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 and APBS
On Thu, Apr 15, 2010 at 10:30 AM, Shiven Shandilya shiven.shandi...@gmail.com wrote: Sorry to be knocking down APBS+PyMOL integration like this, but IMHO VASCo does a stellar job as far as integrating outside programs with PyMOL goes. I initially wrote the PyMOL/APBS plugin for my own use and I now maintain/develop it as a community resource in my limited free time. Despite this, several hundred users (at least) have found it quite helpful in their research, and I've included many newer features based on their feedback. The plugin is certainly not perfect, and I don't mind people knocking it down, but I appreciate it when that knocking down comes with constructive feedback. Additionally, unlike VASCo, the PyMOL/APBS/PDB2PQR toolchain is provided as completely free and open source suite of programs. For many reasons, I believe that free and open source software is vital to to good science. I would strongly urge users to consider such issues before settling on a suite of software products, especially when you're already working with programs like PyMOL and APBS. Cheers, -Michael Good luck! Best, Shiven On Thu, Apr 15, 2010 at 12:01 AM, J. Fleming moloch...@gmail.com wrote: Hi all, I've been trying to get APBS Tools and/or APBSTools2 running for a few weeks now on multiple linux systems (RedHat and Fedora). I've Installed MALOC and APBS Tools. I can start up Pymol through Phenix, load a .pqr generated from a PDB2PQR server, start APBS Tools, set the grid, but when I click on Run APBS I get: ObjectMapLoadDXFile-Error: Unable to open file! If I use the pymol generated PQR option with my .pqr even though it is a PDB2PQR server generated file APBS runs and states X atoms did not have properties assigned and to either remove or fix the atoms. How can I fix them? The problem residues are just regular amino acids; no split confrimations etc. I've also tried editing out the PDBs chain name before converting to the PDB to PQR but that didn't work. Another things I've tried is using APBSTools 2 but it errors as soon as I click set grid with: Error: 2 ... Attribute Error: elec_radius. I really need to get this to work but I have no clue what to try next. Thanks in advance for any thoughts. -Jon -- 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 -- 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 -- 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) -- 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] Some plugin development questions
Hi all,
I'm trying to pretty up the next version of the APBS plugin and I've
run into two issues that I'm hoping others have solved:
1. Does anyone have any experience with PMW's OptionMenu? I've been
trying something where I call an OptionMenu's setitem() and it keeps
failing no matter what I do. Perhaps someone can just point me at some
working sample code.
2. I'm having trouble launching command-line Python scripts from my
plugin on OS X. Scripts complain about things like import time
failing that work from the command line. I have a wrapper function
that works on Windows, OS X and Linux for normal binaries, and I've
included it below. It looks to me like programs launched via PyMOL
(either via os.system or via subprocess.call) just don't get a proper
environment set up, thus causing Python imports to fail, but I'm not
entirely sure.
I typically work around this in an ugly way: I mess around with
sys.path, import whatever.py and then call whatever.main() directly.
This is obviously quite fragile and depends on whatever.py to have a
nice whatever.main() defined. It gets substantially worse when
whatever.py wants lots of things in its own path.
Has anyone else experienced this? Do you know a nice workaround?
Thanks,
-Michael
def run(prog,args):
'''
wrapper to handle spaces on windows.
prog is the full path to the program.
args is a string that we will split up for you.
or a tuple. or a list. your call.
return value is (retval,prog_out)
e.g.
(retval,prog_out) = run(/bin/ls,-al /tmp/myusername)
'''
import subprocess,tempfile
if type(args) == type(''):
args = tuple(args.split())
elif type(args) in (type([]),type(())):
args = tuple(args)
args = (prog,) + args
try:
output_file = tempfile.TemporaryFile(mode=w+) # --
shouldn't this point to the temp dir
except IOError:
print Error opening output_file when trying to run the APBS command.
print Running:\n\tprog=%s\n\targs=%s % (prog,args)
retcode =
subprocess.call(args,stdout=output_file.fileno(),stderr=subprocess.STDOUT)
output_file.seek(0)
#prog_out = output_file.read()
prog_out = ''.join(output_file.readlines())
output_file.close() #windows doesn't do this automatically
if DEBUG:
print Results were:
print Return value:,retcode
print Output:
print prog_out
return (retcode,prog_out)
--
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)
--
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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Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 5
I don't have any MD trajectories on hand at the moment, but can DynoPlot do this? If not, it might be an easy modification. Cheers, -Michael On Sat, Feb 13, 2010 at 9:48 PM, Sean Law magic...@hotmail.com wrote: Hi, Another idea that came to mind while staring at MD trajectories all day is the ability to display measured values (distance, angle, dihedral, etc) in a localized or boxed in area (maybe even under the list of objects). The main use for a measurement area would be to make it easier to monitor allosteric effects. For example, from an MD simulation, if I have a protein that has two distant binding sites and I want to monitor the effects on site A (perhaps, the cavity of site a changes) when the inhibitor binds to site B. In PyMOL, I could measure the distance between the inhibitor and site B but it may simply be too far away to see the changing value as I flip through the frames since it is so far away from site A. If the measurement was instead displayed in its own distinct area, independent of the molecule viewing pane then this could be helpful (or have it displayed in both a separate location as well as the molecule viewing area). Just a thought. Sean -- Windows® phone-your Windows stuff, on the go. See more.http://go.microsoft.com/?linkid=9708119 -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-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) -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-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 Sean, On Fri, Feb 12, 2010 at 12:39 PM, Sean Law magic...@hotmail.com wrote: Hi all, Another feature that I find myself always wanting is a kill script button and/or command. This comes in handy when I am testing a new python script and, accidentally, throw in an infinite loop. It would be nice to have some sort of kill switch not only for python scripts but even for something as simple as ray-tracing. There are times when I am ray-tracing a complicated scene and realize that half-way through the ray-tracing process that something was missing. In that case, I normally have to kill PyMOL and start all over again (and hopefully, I'll have the scene/session saved). Having this function would greatly enhance my productivity. You should see a button labeled Abort at the bottom right of the external GUI window. You can click it to stop the ray tracer. It used to only work if you started the ray tracer by clicking the Ray button in that same window, but it appears to work no matter how you start the ray tracer now (1.2r2). Cheers, -Michael Thanks! Sean -- Not using Hotmail on your phone? Why not? Get it now.http://go.microsoft.com/?linkid=9708120 -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-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) -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-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] Showing electric field lines
Hi all, Someone recently asked me if there was a way to display field lines with PyMOL or with an external plugin. Here's what I wrote: It turns out that PyMOL recently grew the ability to display field lines. After you've run APBS, you'll have a map object called pymol-generated. Try this series of commands from the PyMOL prompt: gradient my_grad, pymol-generated ramp_new my_grad_ramp, pymol-generated color my_grad_ramp, my_grad I'm considering building this into the next version of the plugin. Cheers, -Michael -- 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) -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-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] color by element
have you tried: import util util.cbag util.cbay util.rainbow etc? after you type import util, you can type util. followed by a tab to see the available commands. On Tue, Feb 9, 2010 at 6:09 PM, Nathaniel Echols nathaniel.ech...@gmail.com wrote: On Tue, Feb 9, 2010 at 2:46 PM, Ariel Talavera talav...@cim.sld.cuwrote: How can I use the color by element (HNOS) function present in the GUI, in a script? I don't think there's a single command that does this; I've always done something like this: color grey80, elem c color white, elem h color red, elem o color blue, elem n color orange, elem s and so on (in python, these become 'cmd.color(grey80, elem c)', etc.). I just discovered that there is also a separate color name for each element, e.g. color carbon, elem c will work, but the default coloring scheme seems a bit wacky sometimes (carbon is green, etc.). If there was a convenient way to switch between available color sets (e.g. all of the options available in the menus), that would be awesome. Currently the atom-name colors are hardcoded in C, unfortunately. Nat -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-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) -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-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] Pre-release version of the PyMOL-APBS plugin
Hi all, I've been working with Jason Vertrees on a new version of the PyMOL-APBS plugin and it's now ready for pre-release. There are three big advantages of the new version: * It's been tested modern OS X, Windows and Linux systems and fixes several long-standing bugs. * It allows you to call through to PDB2PQR directly. * It has two visualization panels to aid in showing multiple potential surfaces at once. I've also upped the default maximum allowed memory since typical users have bigger and faster computers these days. The main reason that I'm sending this out now is to get bug reports. I think it runs everywhere, but *please* let me know if you have problems with it. Once it's shown to be stable, it'll be included in the next PyMOL release. A slightly longer list of changes is included below. == How to get it == There are two ways to get the new plugin * If you have subversion installed, you can always get the latest version via svn co https://pymolapbsplugin.svn.sourceforge.net/svnroot/pymolapbsplugin/trunk/pymolapbsplugin * You can download the it from http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py That should give you a file called apbsplugin.py Once you have the plugin, you can install it via PyMOL's plugin installer: Plugin -- Manage Plugins -- Install Note that the plugin will be installed as APBS Tools2 so that you can continue to use your old version. == Longer feature list == * The ability to call through directly to PDB2PQR * More modern apbs input files * Two visualization panels. It's often quite useful to look at two different electrostatic potentials at once. It's also quite useful to look at electrostatic potentials mapped onto two different surfaces at once. Multiple visualization panels makes this a snap: just set up one surface on panel 1 and another surface on panel 2. * Fixes several bugs that caused crashes on both OS X and Linux systems * Increased maximum allowed memory * Switch from os.system to subprocess for running external programs * Deals with paths on Windows properly * Gives better diagnostic information so that PyMOL/APBS developers can find bugs more easily * Lots of internal code cleanup You can find this same information on the PyMOL wiki: http://pymolwiki.org/index.php/User:Mglerner Thanks, -Michael -- 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) -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com___ 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] Rendering plugin
With all of the recent discussion about extensions to the ray command, I thought I'd mention a little plugin I wrote several years ago. You can find it at the bottom of http://sitemaker.umich.edu/carlsonlab/resources.html It's not quite as full-featured as some of the proposed ray extensions, but it does provide a really easy way for you to say I want a 4in x 3in figure at 600dpi. The Ray button raytraces, and the Draw button just draws the image without raytracing (a fast way to see that the height/width look good). It warns you not to have the plugin window on top of your main PyMOL window when you click Ray. That doesn't seem to be necessary anymore, at least on my MacBook Pro. [image: ?ui=2view=attth=12651b51d47cc010attid=0.1disp=attdrealattid=ii_12651b51d47cc010zw] Cheers, -Michael -- 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) ishot-10.png-- 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)
The ray command bugs me, so I'll take a stab at improving it this afternoon. Can someone tell me how to get the size of the current viewport? This solution: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05888.html width,height = cmd.get_session()['main'][0:2] doesn't seem to work for me: PyMOLprint sorted(cmd.get_session().keys()) ['cache', 'color_ext', 'colors', 'editor', 'movie', 'names', 'scene_dict', 'scene_order', 'selector_secrets', 'session', 'settings', 'unique_settings', 'version', 'view', 'view_dict', 'wizard'] -Michael 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)
I think this works. It handles different units (in and cm). If you leave out
width or height, it gets scaled correctly. If you leave them both out, you
get whatever the current viewport size is (is there something better?).
#!/usr/bin/env pymol
from pymol import cmd
def rayy(width=-1,height=-1,dpi=300,units='in',**kwargs):
Slightly better version of the ray command.
You can specify width and height in the units of your choice, e.g.
rayy 3,2,units=in,dpi=300
rayy 3in,2in
rayy 1in, 2 cm, dpi=600
Extra keyword arguments get passed on to the normal ray command.
if type(dpi) in [type('')]: dpi = int(dpi)
in_per_cm = 0.393700787
def todots(x,units,dpi):
if type(x) in [type('')]:
x = x.lower()
if 'in' in x: units = 'in'
elif 'cm' in x: units = 'cm'
x = float(x.replace(units,'').strip())
if units == 'cm': x = x * in_per_cm
elif units == 'in': pass
else: raise ValueError('Unknown units (%s)'%units)
print x,units,dpi
return int(x * dpi)
# How do we get current width/height of viewport? MainSceneGetSize
perhaps
# But it doesn't matter, as PyMOL will autoscale internally for us.
try:
height,width = todots(height,units,dpi),todots(width,units,dpi)
except ValueError:
print Unknown units
return
print 'width',width,'height',height
cmd.ray(width=width,height=height,**kwargs)
#cmd.png(self.filename.getvalue(), dpi=int(self.dpi.getvalue()))
cmd.extend('rayy',rayy)
On Thu, Jan 21, 2010 at 11:52 AM, Michael Lerner
mglerner+sourcefo...@gmail.com mglerner%2bsourcefo...@gmail.com wrote:
The ray command bugs me, so I'll take a stab at improving it this
afternoon.
Can someone tell me how to get the size of the current viewport?
This solution:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05888.html
width,height = cmd.get_session()['main'][0:2]
doesn't seem to work for me:
PyMOLprint sorted(cmd.get_session().keys())
['cache', 'color_ext', 'colors', 'editor', 'movie', 'names', 'scene_dict',
'scene_order', 'selector_secrets', 'session', 'settings', 'unique_settings',
'version', 'view', 'view_dict', 'wizard']
-Michael
On Wed, Jan 20, 2010 at 3:54 PM, Tsjerk Wassenaar tsje...@gmail.comwrote:
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
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--
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)
--
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___
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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)
Here's a slightly improved version. It only kicks in if dpi is specified. I
think that you could make the obvious modifications to the help message and
argument list and use it as a replacement for cmd.ray (as long as you're
aware of the fact that the argument list will be different).
#!/usr/bin/env pymol
from pymol import cmd
def rayy(width=-1,height=-1,dpi=-1,units='in',**kwargs):
Slightly better version of the ray command.
You can specify width and height in the units of your choice, e.g.
rayy 3,2,units=in,dpi=300
rayy 3in,2in
rayy 1in, 2 cm, dpi=600
Extra keyword arguments get passed on to the normal ray command.
Units can be 'in' or 'cm'.
For backwards compatibility, the conversion to dpi (or dots per
centimeter) is only performed when dpi is specified.
if type(dpi) in [type('')]: dpi = int(dpi)
in_per_cm = 0.393700787
def todots(x,units,dpi):
if type(x) in [type('')]:
x = x.lower()
if 'in' in x:
units = 'in'
elif 'cm' in x:
units = 'cm'
x = float(x.replace(units,'').strip())
if (dpi == -1):
return x
if units == 'cm': x = x * in_per_cm
elif units == 'in': pass
else: raise ValueError('Unknown units (%s)'%units)
print '%s%s at %sdpi'%(x,units,dpi)
return int(x * dpi)
# How do we get current width/height of viewport? MainSceneGetSize
perhaps
# But it doesn't matter, as PyMOL will autoscale internally for us when
given -1.
try:
width,height = todots(width,units,dpi),todots(height,units,dpi)
except ValueError:
print Unknown units
return
print 'width',width,'height',height
cmd.ray(width=width,height=height,**kwargs)
cmd.extend('rayy',rayy)
On Thu, Jan 21, 2010 at 2:39 PM, Michael Lerner
mglerner+sourcefo...@gmail.com mglerner%2bsourcefo...@gmail.com wrote:
I think this works. It handles different units (in and cm). If you leave
out width or height, it gets scaled correctly. If you leave them both out,
you get whatever the current viewport size is (is there something better?).
#!/usr/bin/env pymol
from pymol import cmd
def rayy(width=-1,height=-1,dpi=300,units='in',**kwargs):
Slightly better version of the ray command.
You can specify width and height in the units of your choice, e.g.
rayy 3,2,units=in,dpi=300
rayy 3in,2in
rayy 1in, 2 cm, dpi=600
Extra keyword arguments get passed on to the normal ray command.
if type(dpi) in [type('')]: dpi = int(dpi)
in_per_cm = 0.393700787
def todots(x,units,dpi):
if type(x) in [type('')]:
x = x.lower()
if 'in' in x: units = 'in'
elif 'cm' in x: units = 'cm'
x = float(x.replace(units,'').strip())
if units == 'cm': x = x * in_per_cm
elif units == 'in': pass
else: raise ValueError('Unknown units (%s)'%units)
print x,units,dpi
return int(x * dpi)
# How do we get current width/height of viewport? MainSceneGetSize
perhaps
# But it doesn't matter, as PyMOL will autoscale internally for us.
try:
height,width = todots(height,units,dpi),todots(width,units,dpi)
except ValueError:
print Unknown units
return
print 'width',width,'height',height
cmd.ray(width=width,height=height,**kwargs)
#cmd.png(self.filename.getvalue(), dpi=int(self.dpi.getvalue()))
cmd.extend('rayy',rayy)
On Thu, Jan 21, 2010 at 11:52 AM, Michael Lerner
mglerner+sourcefo...@gmail.com mglerner%2bsourcefo...@gmail.com wrote:
The ray command bugs me, so I'll take a stab at improving it this
afternoon.
Can someone tell me how to get the size of the current viewport?
This solution:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05888.html
width,height = cmd.get_session()['main'][0:2]
doesn't seem to work for me:
PyMOLprint sorted(cmd.get_session().keys())
['cache', 'color_ext', 'colors', 'editor', 'movie', 'names', 'scene_dict',
'scene_order', 'selector_secrets', 'session', 'settings', 'unique_settings',
'version', 'view', 'view_dict', 'wizard']
-Michael
On Wed, Jan 20, 2010 at 3:54 PM, Tsjerk Wassenaar tsje...@gmail.comwrote:
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
Re: [PyMOL] Rendering plugin
In keeping with the modern way of doing things, I've 1. put the rendering plugin up on the wiki ( http://pymolwiki.org/index.php/Rendering_Plugin ) 2. put a metric version of the plugin on the same page 3. put the rayy code on my userpage on the wiki ( see my .pymolrc here: http://pymolwiki.org/index.php/User:Mglerner ). If you add it to your .pymolrc, you will be able to type rayy 3 in, 2 in, dpi=300 from the PyMOL command line 4. Followed Luca Jovine's suggestion to change the order of rayy's arguments. Cheers, -Michael On Thu, Jan 21, 2010 at 11:29 AM, Michael Lerner mgler...@gmail.com wrote: With all of the recent discussion about extensions to the ray command, I thought I'd mention a little plugin I wrote several years ago. You can find it at the bottom of http://sitemaker.umich.edu/carlsonlab/resources.html It's not quite as full-featured as some of the proposed ray extensions, but it does provide a really easy way for you to say I want a 4in x 3in figure at 600dpi. The Ray button raytraces, and the Draw button just draws the image without raytracing (a fast way to see that the height/width look good). It warns you not to have the plugin window on top of your main PyMOL window when you click Ray. That doesn't seem to be necessary anymore, at least on my MacBook Pro. [image: ?ui=2view=attth=12651b51d47cc010attid=0.1disp=attdrealattid=ii_12651b51d47cc010zw] Cheers, -Michael -- 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) -- 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) ishot-10.png-- 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] select atoms near electron density
Yes, I believe this is the case. -Michael On Sat, Jan 9, 2010 at 4:20 AM, Jason Vertrees jason.vertr...@gmail.comwrote: Michael, I don't think this is possible with PyMOL. Distance measures are calculated from objects. -- Jason -- Jason Vertrees, PhD jason.vertr...@schrodinger.com PyMOL Product Manager Schrodinger, Inc. On Fri, Jan 8, 2010 at 7:05 PM, Michael Zimmermann micha...@iastate.edu wrote: Dear PyMol users, I wonder if anyone knows a way to select atoms that are near a region of electron density. Say I have a binding pocket in atomic detail, but the ligand binds transiently and non-specifically, so I just have an approximate electron density could for it. Is it possible to select atoms in an object that are near to these density levels? Alternatively, can you turn a map into an object that can be used in this way (fill it with dummy atoms)? Thank you, Michael Zimmermann -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-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 -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-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) -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-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] unable to initialize plugin
This sounds familiar. I think I ran into the same thing with the APBS plugin when upgrading PyMOL at one point. On Fri, Jan 8, 2010 at 11:51 AM, Jason Vertrees jason.vertr...@gmail.comwrote: Ilaria, Which plugin are you trying to use? Also, please beware that scripts and plugins are different and have different methods of install. Lastly are you using PyMOL 0.99, 1.x? -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Fri, Jan 8, 2010 at 9:21 AM, ilaria carlone ilariacarl...@hotmail.com wrote: Hi all, I have some problems after the installation of plugins in PyMOL. I downloaded some plugins from the pymol wiki and copied them in the indicated directory (such as C:\Programs\DeLano Scientific\PyMOL\modules\pmg_tk\startup). I installed them by the PyMOL interface and restarted the program, but, after lauching PyMOL, it returned the following message: Traceback (most recent call last): File /home/scivis/pymol/modules/pmg_tk/PMGApp.py, line 227, in initializePlugins mod.__init__(self) TypeError: module.__init__() argument 1 must be string, not instance Error: unable to initialize plugin (and the name of the plugin...) Can you help me? Maybe it is a trivial problem... Thanks, Ila Ti piace giocare? Tre nuovi giochi Messenger per te! -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-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 -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-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) -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-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] dynamic bonding
I remember this posting from a while ago: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06885.html which may have some clues. --- begin --- Whoops, my bad -- I duped the approval before seeing your repost! Answer: # first create a phony molecular trajectory load $PYMOL_PATH/test/dat/pept.pdb, obj for a in range(2,31): cmd.create(obj,obj,1,a) unbond 5/c, 6/n protect not ((5/c or 6/n) extend 4) sculpt_activate obj, 30 sculpt_iterate obj, 30, 100 smooth obj, 30, 3 # then program a bond-break/re-form movie mset 1 x30 1 -30 30 x30 30 -1 mdo 45: unbond 5/c, 6/n, quiet=1 mdo 100: bond 5/c, 6/n, quiet=1 frame 100 as sticks orient 5-6/n+ca+c mplay # NOTE: only tested on PyMOL 1.2.x Cheers, warren end On Mon, Dec 14, 2009 at 1:12 PM, Jason Vertrees jason.vertr...@gmail.comwrote: Nick, Interesting question. My best guess at this point is that PyMOL can't do what you want. You can load the XYZ file into multiple distinct objects: load myXYZ.xyz, multiplex=1 and each object will be shown with proper bonding. However, the moment you try to combine those into one structure they retain the bonding topology of the first structure. If you change any intermediate state, then they all change. Anyone else? -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Mon, Dec 14, 2009 at 11:30 AM, Nicolas Bock nicolasb...@gmail.com wrote: Hello list, I have a bunch of xyz files that are along a transition path in a molecule. When I load all of them into pymol and step through the individual frames, pymol calculates the bonds only for the initial frame. This leads to wrong bonding in subsequent frames since some atoms move quite a bit during the transition. How can I get dynamic bonding so that bonding is recalculated for each frame? nick -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-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 -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-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) -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-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] Pymol access denied at the NIH
Access to pymol.org has been restored. On Fri, Dec 4, 2009 at 8:25 PM, Michael Lerner mglerner+sourcefo...@gmail.com mglerner%2bsourcefo...@gmail.com wrote: I have no idea why it's been blocked. I filed a ticket with the help desk (by clicking on the link in the middle of the Access Denied page) asking why the site was blocked. I don't see any evidence of hacking on the website. Does anybody else in PyMOL-land have any insight into why the site would be blocked? Assuming that it's just a clerical error, the help desk would probably respond more quickly to a ticket from you than to one from a mere IRTA. Thanks, -Michael On Fri, Dec 4, 2009 at 4:36 PM, Margulies, David (NIH/NIAID) [E] dmargul...@niaid.nih.gov wrote: Pymol website access has been denied at the NIH. How is this happening? -- David H. Margulies, MD, PhD Chief, Molecular Biology Section Laboratory of Immunology, NIAID, NIH Bldg. 10; Room 11N311 10 Center Drive Bethesda, MD 20892-1892 email: d...@nih.gov phone: 301-496-6429 fax: 301-496-0222 ___ The information in this e-mail and any of its attachments are 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 e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. The National Institute of Allergy and Infectious Diseases (NIAID) shall not accept liability for any statement made that are the sender¹s own and not expressly made on behalf of the NIAID by one of its representatives. -- Join us December 9, 2009 for the Red Hat Virtual Experience, a free event focused on virtualization and cloud computing. Attend in-depth sessions from your desk. Your couch. Anywhere. http://p.sf.net/sfu/redhat-sfdev2dev ___ 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) -- 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) -- Join us December 9, 2009 for the Red Hat Virtual Experience, a free event focused on virtualization and cloud computing. Attend in-depth sessions from your desk. Your couch. Anywhere. http://p.sf.net/sfu/redhat-sfdev2dev___ 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 access denied at the NIH
I have no idea why it's been blocked. I filed a ticket with the help desk (by clicking on the link in the middle of the Access Denied page) asking why the site was blocked. I don't see any evidence of hacking on the website. Does anybody else in PyMOL-land have any insight into why the site would be blocked? Assuming that it's just a clerical error, the help desk would probably respond more quickly to a ticket from you than to one from a mere IRTA. Thanks, -Michael On Fri, Dec 4, 2009 at 4:36 PM, Margulies, David (NIH/NIAID) [E] dmargul...@niaid.nih.gov wrote: Pymol website access has been denied at the NIH. How is this happening? -- David H. Margulies, MD, PhD Chief, Molecular Biology Section Laboratory of Immunology, NIAID, NIH Bldg. 10; Room 11N311 10 Center Drive Bethesda, MD 20892-1892 email: d...@nih.gov phone: 301-496-6429 fax: 301-496-0222 ___ The information in this e-mail and any of its attachments are 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 e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. The National Institute of Allergy and Infectious Diseases (NIAID) shall not accept liability for any statement made that are the sender¹s own and not expressly made on behalf of the NIAID by one of its representatives. -- Join us December 9, 2009 for the Red Hat Virtual Experience, a free event focused on virtualization and cloud computing. Attend in-depth sessions from your desk. Your couch. Anywhere. http://p.sf.net/sfu/redhat-sfdev2dev ___ 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) -- Join us December 9, 2009 for the Red Hat Virtual Experience, a free event focused on virtualization and cloud computing. Attend in-depth sessions from your desk. Your couch. Anywhere. http://p.sf.net/sfu/redhat-sfdev2dev___ 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] APBS plugin woes
We solved the problem this afternoon. The version of APBS that comes with PyMOL does not work on Tiger (10.4). Neither does the universal binary of apbs-1.2.1b available on sourceforge. An older version of apbs (0.5) worked. We are in the middle of installing APBS via MacPorts, as it seems like that should work too. I've added some troubleshooting instructions to both http://pymolwiki.org/index.php/APBS and http://pymolwiki.org/index.php/User:Mglerner On Mon, Nov 30, 2009 at 2:21 PM, David Garboczi dgarbo...@niaid.nih.govwrote: I download and install macpymol-1_2r2.tgz. I make a copy of MacPyMOL.app and rename it PyMOLX11Hybrid.app and fire it up. Load a pdb file after removing HETATM lines. Open APBS Tools and set grid: Log: Maximum number of grid points exceeded. Old grid dimensions were [129, 97, 129] Fine grid points rounded down from [117, 87, 117] New grid dimensions are [97, 65, 97] APBS Tools: coarse grid: (76.908,61.259,77.489) APBS Tools: fine grid: (65.240,56.035,65.582) APBS Tools: center: (-22.620,-1.106,-3.967) APBS Tools: fine grid points (97,65,97) Click Run APBS, see hydrogens appear, see residues being selected and unselected, then the display says: Log: ObjectMapLoadDXFile-Error: Unable to open file! ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist? Help? PowerBook, PPC, 10.4.11 Dave -- David N. Garboczi, PhD Phone: 301-496-4773 Head, Structural Biology Section (SBS) Research Technologies Branch (RTB) National Institute of Allergy and Infectious Diseases (NIAID) National Institutes of Health (NIH) Twinbrook 2/Room 110 12441 Parklawn Drive Rockville, Maryland 20852-1742 Fax:301-402-0284 Email: dgarbo...@niaid.nih.gov 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 e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. The National Institute of Allergy and Infectious Diseases (NIAID) shall not accept liability for any statement made that are the sender's own and not expressly made on behalf of the NIAID by one of its representatives. -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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) -- Join us December 9, 2009 for the Red Hat Virtual Experience, a free event focused on virtualization and cloud computing. Attend in-depth sessions from your desk. Your couch. Anywhere. http://p.sf.net/sfu/redhat-sfdev2dev___ 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] APBS plugin woes
Can you go to the Program Locations tab and find out which version of APBS you're using? There's a problem with the one in /Applications/PyMOLX11Hybrid.app/pymol/freemol/bin. I've added instructions for fixing this problem to http://pymolwiki.org/index.php/User:Mglerner . The instructions are near the top of the page, under APBS Plugin FAQ. Could you try them out and see if they work for you? Thanks, -Michael On Mon, Nov 30, 2009 at 2:21 PM, David Garboczi dgarbo...@niaid.nih.govwrote: I download and install macpymol-1_2r2.tgz. I make a copy of MacPyMOL.app and rename it PyMOLX11Hybrid.app and fire it up. Load a pdb file after removing HETATM lines. Open APBS Tools and set grid: Log: Maximum number of grid points exceeded. Old grid dimensions were [129, 97, 129] Fine grid points rounded down from [117, 87, 117] New grid dimensions are [97, 65, 97] APBS Tools: coarse grid: (76.908,61.259,77.489) APBS Tools: fine grid: (65.240,56.035,65.582) APBS Tools: center: (-22.620,-1.106,-3.967) APBS Tools: fine grid points (97,65,97) Click Run APBS, see hydrogens appear, see residues being selected and unselected, then the display says: Log: ObjectMapLoadDXFile-Error: Unable to open file! ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist? Help? PowerBook, PPC, 10.4.11 Dave -- David N. Garboczi, PhD Phone: 301-496-4773 Head, Structural Biology Section (SBS) Research Technologies Branch (RTB) National Institute of Allergy and Infectious Diseases (NIAID) National Institutes of Health (NIH) Twinbrook 2/Room 110 12441 Parklawn Drive Rockville, Maryland 20852-1742 Fax:301-402-0284 Email: dgarbo...@niaid.nih.gov 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 e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. The National Institute of Allergy and Infectious Diseases (NIAID) shall not accept liability for any statement made that are the sender's own and not expressly made on behalf of the NIAID by one of its representatives. -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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) -- Join us December 9, 2009 for the Red Hat Virtual Experience, a free event focused on virtualization and cloud computing. Attend in-depth sessions from your desk. Your couch. Anywhere. http://p.sf.net/sfu/redhat-sfdev2dev___ 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] segmentation fault!
Hi, I can try to look into this, although I'm not sure what's causing it. Can you tell me - what version of PyMOL you have and how it was installed - what version of APBS you have and how it was installed - when exactly the segmentation fault happens (are you working with a particular PDB file, etc.) Thanks, -Michael On Sun, Nov 22, 2009 at 4:00 PM, Mehdi Talebzadeh Farooji mahdi...@yahoo.com wrote: Dear All, I run pymol on laptop ubuntu 9.10 with ATI raedon gaphic card. when I try to call plugin of pymol for APBS, pymol crashes with segmentation fault message. Every suggestion would be welcomed! Thanks, Mehdi __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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) -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ 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] Creating a single PDB from two PDB - ala docking by hand
I definitely remember some mode where PyMOL would show good/bad contacts with red/green dots, but I can't seem to figure it out now. It was in Warren's talk as he was manually docking in a ligand. I searched, but couldn't figure it out myself. Does anyone know how to put PyMOL into that mode? Cheers, -Michael On Thu, Sep 3, 2009 at 12:04 PM, H. Adam Steinberg a...@steinbergs.uswrote: Bring up both pdb files in one session, orient the ligand by going to editing mode and using the shift key with the left mouse button (3 button mouse mode) to move just the ligand. Once you have it in the position you want, type select all in the command line and then hit enter, In the A menu for the (sele) you just created pick copy to object. PyMOL will create a new pdb with all of the coordinates of the two pdb files as they are positioned on screen. Rename it if you'd like, and save the new pdb out from the File menu/save molecule. Mark Benson wrote: Dear All, I am trying to build a single PDB file from two different PDB files. One PDB has a small organic ligand, and the second PDB contains amino acid side chains from an active site. I load both PDB files, but I want to freeze the orientation of the amino acid side chains PDB ( not move it), and then place and orient the ligand PDB in a certain pose with respect to the amino acid side chains. Ideally, I would then like to save the coordinates for both the amino side chains and the ligand coordinates to a single PDB file. In the long run, I want to run a simple minimization on an possible active site cluster and I want to get a feel for the energetics of the ligand in the active site. I don't like working with MOLDEN or some of the other suites out there and I wanted to try this with PyMOL. I've gone through the manual, the web, pymolwiki, the masking and protecting options, and I've tried examining the use of frames and split_states, but I haven't come up with anything. I've heard about a demo that Warren DeLano put on for the ACS where, as part of the demo, he showed off some toy example where he docked a ligand in by hand, complete with having PyMOL show red/green dots for steric clashes/matches. Any ideas? -Mark -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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 -- ___ H. Adam Steinberg Artist, Scientist http://adam.steinbergs.us Information Technology and Media Center Department of Biochemistry University of Wisconsin-Madison 433 Babcock Drive Madison, WI 53706 608/265-4982 ___ -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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) -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ 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] problems with apbs/pqr
Whoops! I accidentally replied only to James, rather than to the whole list. PyMOL has some trouble with assigning charges. PDB2PQR handles it, but manages to generate a bad PQR (missing the space between some columns with leading minus signs, e.g. -100.2345-100.2345). Fixing the PQR file by hand fixes the problem. -michael On Wed, Aug 5, 2009 at 11:35 AM, Warren DeLano war...@delsci.com wrote: James, It sounds like there mayy be something other than canonical amino acids in your structure which might need to be removed prior to performing a calculation. These may be alternate conformations of amino acid side chains, ligands, or other unrecognized groups which cannot be processed for APBS. Cheers, Warren -Original Message- From: James Whittle [mailto:whit...@mit.edu whit...@mit.edu] Sent: Wed 8/5/2009 5:01 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] problems with apbs/pqr Hi all, My apologies if this has been covered by this list before, but I couldn't find mention of it: I'm trying to calculate an electrostatic surface for my protein. The APBS Tools plug-in crashes with the message: WARNING: 502 atoms did not have formal charges assigned WARNING: 1051 atoms did not have properties assigned This happens whether I use a pqr file from PDB2PQR or the PyMol generated PQR. I'm running OS X (Intel), Pymol version 1.2r0. I also tried it though on a linux machine, and got the same error. This plug-in works fine with several other coordinate files. I tried removing the chain ids from the pdb file, but that did not help. Can anyone offer any advice on this? --James -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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) -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ 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] is this how i would write a coding sequence?
Aha! I knew there was a better way of doing this, but I was stuck on a machine that only had an old version of PyMOL. Assuming you're using PyMOL 1.0 or newer, you can just use pseudoatom. To create a sphere of radius 10.0 at the xyz position (50.0,60.0,12.0), just do this: pseudoatom mysphere, pos=[50.0,60.0,12.0], vdw=[10.0] it will appear as a kind of cross at first. to show it as a sphere, type show spheres, mysphere to make it partially transparent, type set sphere_transparency, 0.5, mysphere The sphere that you get will look kind of blocky. You can get a perfect sphere by raytracing, e.g. typing ray If you don't mind the fact that it won't be transparent, you can get a perfect sphere in the normal viewer by typing set sphere_mode, 5 To go back to normal spheres after you've done that, type unset sphere_mode I think this will be easier than the other way I recommended. Cheers, -michael On Tue, Jul 7, 2009 at 1:55 PM, Benjamin Michael Owen owe...@marshall.eduwrote: I'm trying to use a suggestion another pymol user sent to create a sphere of a specific size in a pdb file. Is this the correct coding? I have no experience doing any kind of programming so I am not sure if I did this right. I put the text I entered in in red if that helps anything. ben create sphere, resi 24 and resi 864 create a new object from resi 864 alter sphere, vdw=10.0 # 28.5 rebuild # necessary if spheres have already been shown show spheres, sphere alter_state 1, sphere, x,y,z = 50,60,10 # set desired x,y,z coords set sphere_transparency, 0.5, sphere # make it transparent zoom ray -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/blackberry ___ 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) -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/blackberry___ 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 question
I'm sure there's a way to actually draw a circle, but for your particular use it might be better to use a sphere. If you're comfortable with python scripting, you can use CGO objects. If not, you might do something like this: fetch 1hhp create thing, resi 24 and name ca # create a new object from some single atom selection alter thing, vdw=10.0 # set desired radius rebuild # necessary if spheres have already been shown show spheres, thing alter_state 1, thing, x,y,z = 50,60,10 # set desired x,y,z coords set sphere_transparency, 0.5, thing # make it transparent zoom ray you can also use something like select + within to select all residues within a cutoff, but I got the impression you wanted a nice visualization. Hope that helps, -michael On Mon, Jul 6, 2009 at 5:01 PM, Benjamin Michael Owen owe...@marshall.eduwrote: Does anyone know how to draw a circle with a given radius in pymol? I have a distance that I want to use to see what residues lie on the end of that radius, but I have no idea how to write the command to draw the circle. Could someone help me please? -- ___ 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) -- ___ 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] Missing external GUI and search for the APBS plug-in for PyMOL
I've seen this before when something went wrong with launching X11. Have you tried launching X11 first, verifying that it works, and then launching PyMOLX11Hybrid while X11 is already running? On Fri, Mar 13, 2009 at 1:15 PM, Atreyi Chatterjee chatterj...@mail.nih.gov wrote: Hi, I was trying to find out how to locate and use the APBS plug-in for MacPyMOL and when I mailed to the APBS-users list I was advised to rename MacPyMOL.app to PyMOLX11Hybrid.app which would make the APBS plug-in work in PyMOL. I tried following this suggestion and being a complete novice in this field I might be missing some simple points here or making some silly mistakes. I would be really grateful if you share your thoughts with me. My issue is that once i rename MacPyMOL.app to PyMOLX11Hybrid.app I end up opening a version of PyMOL that has the the top area or the External GUI missing. Only the bottom window containing the Internal GUI opens up. Since the external GUI has all the user friendly menu bars for a layman like me it is more familiar and easier to work with. The internal GUI has the secondary command line and it would be almost impossible for a person like me to work using this only. I am wondering if the PyMOLX11 version works only with commands only? Or, is it something that I have done that made the external GUI disappear!! This is what i didwhen i tried opening the PyMOLX11Hybrid on my Mac, it asked me to choose an application and asked for the location of X11. I specified it from the applications folder and it opened up w/o the external GUI. W/o the external GUI i cannot access the wizard menu to access the APBS tools what am i saying, w/o it I cannot even open a file now!!! I do not have multiple monitors connected to my computer and I am not using Leopard with spaces enabled. I cannot figure out why the top GUI is missing from my screen! Is there a way to bring it back? Please help. Thanks Atreyi Atreyi Chatterjee, Ph. D. Section on Eukaryotic Transposable Elements NIH /NICHD/PCRM Bldg. 18T, Rm # 106 Bethesda, MD 20892 P: (301)-402-1532, F: 301-496-4491 *chatterj...@mail.nih.gov*** chatterj...@mail.nih.gov -- Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- 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)
Re: [PyMOL] select by absolute coordinate
Hi, I have a couple of quick notes about your specific application: This works well when bilayers are flat. So, it works well for small bilayers and it works well at the beginning of a simulation. For medium to large bilayers, undulations throughout the simulation will cause this algorithm to break. Here are some other things that don't work: - selecting all lipids where atom X is higher than atom Y. In longer simulations, lipids wiggle around enough that the heads can tilt and the tails can even be higher than the heads. - same as above, but looking at the center of mass of the head vs. the COM of the tail. This fails for the same reason. It turns out that lipids really wiggle a lot. - etc. These are easy errors to miss because the algorithms work well at the beginning of the simulation, so even a quick visual examination won't show the problems. In my experience, the easiest thing to do is to use your method on the first frame of a simulation, inspect the selection visually, and then write it out explicitly for use in subsequent frames. You probably know all of this, but I thought I'd mention it in case someone was tempted to just take your code and apply it individually to each frame of a simulation without really thinking about it. Unfortunately, I've seen people make this particular error a few times (in both VMD and C), and usually you can't tell they're making it just by reading their Methods section :(. Cheers, -michael On Wed, Mar 4, 2009 at 6:04 AM, Höfling Martin martin.hoefl...@gmx.dewrote: Am 04.03.2009 um 06:46 schrieb Warren DeLano: Hey Warren, It is remarkable that a question like this hasn't come up before, but it reveals a rather large whole in PyMOL's selection language: though we have some proximity operators, we are not currently able to select atoms based on absolute or relative coordinate vector relationships. So the present answer to your question appears to be no. Sorry about that! Just to give the application to my question: If you wanna select the upper leaflet of a bilayer - an easy method - shown to me in VMD is to select by residue all Phosphor atoms with e.g. z 40... Well I scripted a bit around it which worked in my case: def leafletIndex(): ''' Create leaflet indices for upper and lower bilayer, based on Phosphor atoms ''' cmd.delete(Phosphor) cmd.delete(UpperLeaflet) cmd.delete(LowerLeaflet) cmd.select(Phosphor,name P*) ext=cmd.get_extent(Phosphor) lower=ext[0][2] upper=ext[1][2] middle=upper-lower atoms = cmd.get_model(Phosphor) cmd.select(UpperLeaflet,None) cmd.select(LowerLeaflet,None) for at in atoms.atom: if at.coord[2] middle: cmd.select(UpperLeaflet,UpperLeaflet or index %d%at.index) else: cmd.select(LowerLeaflet,LowerLeaflet or index %d%at.index) cmd.select(UpperLeaflet,byres UpperLeaflet) cmd.select(LowerLeaflet,byres LowerLeaflet) cmd.deselect() Best Martin -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- 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)
Re: [PyMOL] How to display two or multiple eleectrostatic maps simultaneously with PyMol?
Hi, The current version of the APBS Plugin (http://www.umich.edu/~mlerner/PyMOL) has two visualization panes. You can use them to control two separate molecule/map combinations. Please let me know if you need more assistance, -Michael On Thu, Jun 26, 2008 at 10:28 PM, Youzhong Guo youzhong...@gmail.com wrote: Dear All, I have difficulty to display two electrostatic maps with PyMol at the same time . I can correctly display one map with pdbset1.pqr and pdbset_1.dx as in slide No.1. I can also correctly display one map with pdbset3.pqr and pdbset_3.dx as in slide No.2. However, when I tried to load all of those four files with PyMol, what I can get is as in slide No. 3 or No.4. As you can see in slide No.3 or No.4 the map is not correct as expected. Please download my files from the following link and see if you can simultaneously display two maps as shown in slide No.1 and No.2 with PyMol. https://webspace.utexas.edu/yg387/Electron_static_potential.zip Thanks in advance, Youzhong - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909 Rockville, MD 20852 http://www.umich.edu/~mlerner
[PyMOL] How to view electron densities from the PDB
Hi, This is probably a fairly basic question, but I'm stumped. I want to visualize electron densities along with my PDB file. So, say I'm interested in 2DJX. I go to the PDB and download 2DJX.pdb and 2djx-sf.cif. PyMOL doesn't seem to read the CIF file (?), so I downloaded and installed the PDB's tool sf-convert (http://sw-tools.pdb.org/apps/SF-CONVERT/index.html). I tried sf-convert -i CIF -o Xplor -sf 2djx-sf.cif but got some errors about the input format. sf-convert -i mmCIF -o Xplor -sf 2djx-sf.cif seemed to work (it produced a .Xplor file with what looks like data to me). However, PyMOL gives me errors when I try to load the resulting .xplor file. This may not be directly related to PyMOL, but I'm hoping it's a common enough task that someone can point me in the right direction. Thanks, -michael -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909 Rockville, MD 20852 http://www.umich.edu/~mlerner
Re: [PyMOL] drawing axes
@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909 Rockville, MD 20852 http://www.umich.edu/~mlerner
Re: [PyMOL] how to get version?
pymol.cmd.get_version() (i kinda expected pymol.__version__ to work, but it doesn't) On Tue, Jun 3, 2008 at 3:35 PM, Matthew O'Meara mattjome...@gmail.com wrote: Hi All, Is there a simple way to test which version of pymol is begin used in a script? Specifically I would like to know if it is 1.0 or =1.0 Thanks, Matt - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909 Rockville, MD 20852 http://www.umich.edu/~mlerner
Re: [PyMOL] interior protein-surfaces
I'm not sure it's exactly what you're looking for, but this seems similar: http://hollow.sourceforge.net/ On Tue, May 27, 2008 at 4:53 PM, Thomas S. Leyh, Ph. D. l...@aecom.yu.edu wrote: From time to time I find it valuable to view the suface of a ligand-binding pocket looking out from the surface's interior. This is accomplished in a variety of ways - principally, zooming and clipping. It would be wonderful to be able to represent just the skin of the active site wrapping around the ligands, like a sac - this seems quite difficult to achieve. A related problem is that ray-ing a surface that has been clipped yields a collection of odd surface regions that represent poorly the non-ray-ed version - it is as if the resolution of the ray it too gross to capture the clipping edges. Advice appreciated. Thanks, Tom Leyh - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909 http://www.umich.edu/~mlerner
Re: [PyMOL] Will Pymol participate in Google Summer of Code 2008?
On Fri, Mar 7, 2008 at 5:04 PM, DeLano Scientific del...@delsci.info wrote: So from where I sit, the obvious open-source candidates are: APBS (electrostatics -- improve the current plugin) Please let me know if anyone decides to do this. I have an (unreleased) improved version, and several ideas for how to improve it further. I'd be glad to help out. -michael RDKit (cheminformatics, depiction, UFF cleanup, etc.) mengine (MMFF small molecule cleanup) mpeg_encode (MPEG movie production on Linux, etc.) GIMP (image manipulation) Blender (general-purpose 3D modeling animation) Jmol (publishing visualizations inside of web pages) Firefox (ditto) MMTK (molecular mechanics -- Python/flexible) GROMACS (molecular mechanics -- C/fast) OpenOffice (escape from the microsoft hegemony) (NOTE: work is already underway for mpeg_encode and mengine...) Are there other key open-source packages we might specifically target for integration with PyMOL, either through SOC or beyond? Although there are many niche tools, from a prioritization standpoint, efforts should focus on integrations that will impact the largest potential user base. So what hypothetical integrations would be useful to virtually all medicinal chemists, all structural biologists, all movie-makers, all paper-writers, and so on? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: Anders Norgaard [mailto:anders.norga...@gmail.com] Sent: Wednesday, March 05, 2008 1:10 PM To: DeLano Scientific Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Will Pymol participate in Google Summer of Code 2008? On Wed, Mar 5, 2008 at 9:57 PM, DeLano Scientific del...@delsci.info wrote: Anders, No plans at present, but hey, it is still one whole week before a week before the deadline! :o) Anyone out there with sufficient bandwidth to mentor? Hmm... Perhaps a nucleating effort on Jmol / PyMOL interporability would make a good SOC project? Well, there is also a whole list of stuff in your PyMOL By Popular Demand Survey (Jan 2008) mail, perhaps some of these could be bundled into a project? - An ActiveX Control - 2D structure display - More documentation, screencasts, tutorials. - Browser plugins - Direct MPEG movie export - Direct WinAVI movie export - Structure cleanup energy minimization - Objects/states split over multiple windows (side by side views) - Multi-line text annotations in scenes - APBS bundled witih PyMOL - Per-object Z clip - native Windows user interface in a single window - Undo - Improved molecular builder - Better RigiMOL integration - MOPAC integration - Sequence alignment editing - 3D PDF export - Cleaned up matrix transformation interface - Blender integration - Nucleic acid building - Calculate surface areas and volumes - Secondary structure display in sequence viewer - Scene buttons / sorter - Movie slider ala Cinema4D/Maya/3DSMax - Drag drop programming of object motions or Pymol MMTK integration? Best, Anders Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Anders Norgaard Sent: Wednesday, March 05, 2008 8:53 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Will Pymol participate in Google Summer of Code 2008? Hi, I guess that it is one of the great ways to catch young new contributors. http://code.google.com/soc/2008/ Best, Anders -- --- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909 http://www.umich.edu/~mlerner
Re: [PyMOL] Command-line arguments when using PyMOL to launch a script
Hi,
First, the initial error you were seeing was a syntax error:
from sys import argv
my_argv =3D argv[argv.index(--):]
print my_argv[1], my_argv[2]
is failing because of the word 3D
Second, that used to fail on Linux systems anyway (it worked on some
other systems). I tend to use optparse, which often requires things to
live in sys.argv. Here's my current workaround:
#argv = sys.argv[sys.argv.index('--') + 1:]
try:
argv = sys.argv
except AttributeError:
argv = pymol_argv
sys.argv = pymol_argv # this is necessary for optparse to
handle the --help option.
try:
argv = argv[argv.index('--') + 1:]
except IndexError:
argv = []
options,args = parser.parse_args(args=argv)
I haven't re-tested Linux recently, though. It might be that the
pymol_argv workaround is not necessary anymore.
-michael
--
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909
http://www.umich.edu/~mlerner
Re: [PyMOL] Distance labels
An object whose name begins with an underscore will not appear in the menu. On Feb 11, 2008 3:13 PM, Toni Pizà servo...@gmail.com wrote: Hi! When I create a distance in a pymol session, an object called dist n is created, and a label with there name is shown at the right of the screen, with the other objects loadeds. Can I create a dist, and render the dotted line at the screen, without having the label in the right menú? Thanks a lot, and sorry for my poor english! -- Two of the most famous products of Berkeley are LSD and Unix. I don't think that this is a coincidence. http://servomac.blogspot.com - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909 http://www.umich.edu/~mlerner
Re: [PyMOL] apbs plugin for macpymol
I would like to use apbs from within PyMOL. I have downloaded and installed the latest version of apbs, and apbs_tools.py exists in $PYMOL_PATH/modules/pmg_tk/startup/. However, I find no plugins entry in any of the PyMOL menus. I think that you need to rename the application bundle to PyMOLX11Hybrid in order to use plugins. Am I blind or daft? But the question I'd really like to have answered is how do I get abps to work. I would suggest 1) register APBS here http://agave.wustl.edu/apbs/download/ 2) Install fink ( http://finkproject.org/ ) and then use it to install apbs (e.g. by typing fink install apbs on the command line). hope that helps, -michael I'm using educational MacPyMOL, which integrates and extends Open-Source PyMOL 1.0r1. Thanks. Andreas - SF.Net email is sponsored by: Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner
[PyMOL] Trouble making pictures in a script
Hi, I have a Python script that sets a system up and then calls cmd.png() to render an image. I use it to process several files at a time, and there's no need to look at it while it's working, so I use pymol -qcr myscript.py to launch it. It works fine when I ray trace things, but if I just set the system up and call cmd.png(), I get this error: ScenePNG-WARNING: invalid context or no image. Calling cmd.draw() instead of cmd.ray() doesn't seem to fix things. Any ideas? Some of the systems are big enough that cmd.ray() fails, so I'd like to be able to find a workaround. Thanks, -michael -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner
Re: [PyMOL] APBS-electrostatics
It looks like quite a few people are actually still using the electrostatics wizard, so I updated the code on my website (http://www.umich.edu/~mlerner/PyMOL). For what it's worth, I just use the visualization pane of the APBS plugin these days, but I understand if the wizard is a little cleaner for some purposes. -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner On 10/4/07, DeLano Scientific del...@delsci.info wrote: Gianluigi, The API changed in PyMOL 1.0 in order to accomodate multiple PyMOL instances in a single Python interpreter -- your wizard needs to be updated so that the init method takes a _self keyword argument: def __init__(, _self=cmd): ... -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor! -WLD From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Gianluigi Caltabiano Sent: Thursday, October 04, 2007 7:55 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] APBS-electrostatics Hi everybody, I am trying to use the electrostatic wizard to read some .dx file I made. It always worked..since I up-graded to pymol 1.0. Now it doesn't work ( I have already checked the modification in __init__.py file, it's fine). The message it give to me is: Traceback (most recent call last): File C:\Archivos de programa\DeLano Scientific\PyMOL/modules\pymol\parser.py, line 251, in parse self.result=apply(layer.kw[0],layer.args,layer.kw_args) File C:\Archivos de programa\DeLano Scientific\PyMOL/modules\pymol\wizarding.py, line 86, in wizard r = _wizard(name,arg,kwd,0) File C:\Archivos de programa\DeLano Scientific\PyMOL/modules\pymol\wizarding.py, line 45, in _wizard wiz = apply(getattr(mod_obj,oname),arg,kwd) TypeError: __init__() got an unexpected keyword argument '_self' Thank you for your help Gianluigi Caltabiano L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] electron density map representation as dot
You can do this with the isodot command. Are you using the PyMOL-APBS plugin to generate or view electron density maps? If so, would you like me to add dot representations to the plugin in the next release? Thanks, -michael -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner On 8/15/07, shivesh kumar shivesh_...@yahoo.com wrote: Dear all How can the dot representation of electron density map is made as in the figure in attachment,I know the mess representation through isomesh command.Please suggest.Thanx in advance. Shivesh kumar shivesh Be a better Heartthrob. Get better relationship answers from someone who knows. Yahoo! Answers - Check it out. - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Why can't I get to sys.argv on Linux?
Hi, I'm using PyMOL as a front end to a few scripts. So, I need to get my hands on sys.argv to process the command-line arguments. On OS X, everything works just like I'd expect. However, on Linux, I can't get sys.argv. Here's a very simple Python script: #!/usr/bin/env python import sys print dir(sys) print sys.argv When I run pymol -cr ./my_script.py on Linux, I get this: PyMOLrun ./x.py,main ['__displayhook__', '__doc__', '__excepthook__', '__name__', '__stderr__', '__stdin__', '__stdout__', '_getframe', 'api_version', 'builtin_module_names', 'byteorder', 'call_tracing', 'callstats', 'copyright', 'displayhook', 'exc_clear', 'exc_info', 'exc_type', 'excepthook', 'exec_prefix', 'executable', 'exit', 'exitfunc', 'getcheckinterval', 'getdefaultencoding', 'getdlopenflags', 'getfilesystemencoding', 'getrecursionlimit', 'getrefcount', 'hexversion', 'maxint', 'maxunicode', 'meta_path', 'modules', 'path', 'path_hooks', 'path_importer_cache', 'platform', 'prefix', 'setcheckinterval', 'setdlopenflags', 'setprofile', 'setrecursionlimit', 'settrace', 'stderr', 'stdin', 'stdout', 'version', 'version_info', 'warnoptions'] Traceback (most recent call last): File /users/mlerner/src/pymol/modules/pymol/parser.py, line 287, in parse parsing.run_file(exp_path(args[nest][0]),__main__.__dict__,__main__.__dict__) File /users/mlerner/src/pymol/modules/pymol/parsing.py, line 407, in run_file execfile(file,global_ns,local_ns) File ./x.py, line 4, in ? print sys.argv AttributeError: 'module' object has no attribute 'argv' PyMOL: normal program termination. While pawing around in the PyMOL sources, I found that pymol_argv shows up. It seems to be what I want, but I don't know how stable it is. Am I supposed to use it instead of sys.argv? Thanks, -michael -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner
[PyMOL] Are there any feature requests for the PyMOL-APBS plugin?
Hi, I'm working on an update to the PyMOL-APBS plugin. Are there any features that you would like to see included? As an example, I'm including the ability to use PDB2PQR to generate PQR files in the next version. Please request anything you'd like, no matter how trivial/difficult you think it might be to implement (that's not a promise that I'll implement it .. just that I'll consider it :) ). Thanks, -Michael Lerner -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner
[PyMOL] Command-line arguments when using PyMOL to launch a script
Hi,
I have a script that uses PyMOL to aid with a lot of calculations. So,
I run the script like this:
pymol -c script.py
The script has grown so that it has a lot of options. Right now, I
edit the script every time I want to change them. If it were a normal
Python script, I'd run it like
script.py --do=something --when=now
Is there a standard way to do this via PyMOL? Ideally, I'd like to say
pymol -qcr script.py --do=something --when=now
and have script.py think that sys.argv == ['script.py',
'--do=something', '--when=now'].
I pawed through pymol.invocation.py, and it looks like PyMOL respects
the convention where it won't parse arguments after a '--', so my
current workaround is to launch things like
pymol -qcr script.py -- -do=something --when=now
and then this in my script:
argv = sys.argv[sys.argv.index('--') + 1:]
...
# parse with optparse
options,args = parser.parse_args(args=argv)
So, is there a more standard way of doing this? If not, hopefully
google will find this for me the next time I have this question :).
Thanks,
-Michael
--
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner
Re: [PyMOL] APBS
Hi, Can you try installing the most recent version of my plugin from http://www-personal.umich.edu/~mlerner/Pymol/index.html (you can use the normal Install Plugin menu option .. there's no need to do things by hand anymore)? It fixes some problems and gives better error messages on others. Thanks, -Michael -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner On 5/24/07, Oganesyan, Vaheh oganesy...@medimmune.com wrote: I'll appreciate some help with APBS plugin. In both Win or Lin the same error appears: ObjectMapLoadDXFile-Error: Unable to open file! After googling with this error message I've checked all of the possibilities: Map file is loaded OK, folders with apbs.exe and psize.py files do not contain blanks, the *.pqr file is created using pdb2pqr server with and without chain identifier. At this point I do not know what else to try. Before (about 1 year ago) I've used it with no problems. Could someone point me to the problem? Windows version is 0_99rc6 installed using binaries. Thanks in advance. Vaheh Oganesyan - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Single transparent sphere
The pseudoatom business looks very cool. I'll have to try it out.
In the meantime, I wanted to mention that you certainly can make
transparent CGOs. Here's some code that I wrote to visualize dock
output in our lab. The files it reads in have lines that look like
junk x y z r junk temp junk
Where x,y,z are the coordinates, r is the radius and temp is some
index that we use to look up colors. If you save this in a file,
you'll have a new command, sds, that will read in such a file and show
the output as spheres. Transparency defaults to 0.4, but you can
change it.
-michael
#!/usr/bin/env python
Use PyMOL to show DOCK spheres
from pymol import cmd,cgo
colors = {'1':[.66,.66,.66],#'grey'
'2':[1,0,0],#'red',
'3':[.55,0,0],#'dark red',
'4':[0.65,1,1],#'blue2',
'5':[.25,.88,.82],#'blue7',
'6':[0.004,.55,.55],#'blue8',
'7':[0.004,.55,.55],#'blue8',
'8':[0,1,1],#'blue13',
'9':[0,1,1],#'blue13',
'11':[0.60,.98,.60],#'pale green',
'12':[0.56,.93,.56],#'light green',
'13':[.20,.80,.20],#'lime green',
'14':[.23,.70,.44],#'green8',
'15':[.23,.70,.44],#'sea green',
'16':[.18,.55,.34],#'sea green',
'17':[.18,.55,.34],#'green',
'18':[0,.5,0],#'forest green',
'19':[0,.5,0],#'forest green',
'20':[.13,.55,.13],#'dark green',
'21':[.13,.55,.13],#'dark green',
}
def graph_temp_via_cgo(name,data,transparency=0):
Data should be [x,y,z,r,temp] where
x,y,z are the coordinates,
r is the radius
temp is something like temperature that we
use to look up colors.
obj = []
for x,y,z,r,temp in data:
#transparency = (y/200.0)
obj.extend( [ cgo.ALPHA,1-transparency])
obj.extend( [ cgo.COLOR] + colors[temp])
obj.extend( [ cgo.SPHERE,x,y,z,r] )
cmd.load_cgo(obj,name,1)
return name
def dock_file_to_data(filename):
data = []
f = file(filename)
for line in f:
if not line.strip():
continue
if line.startswith('#'):
continue
junk1,x,y,z,r,junk2,temp,junk3 = line.split()
x,y,z,r = map(float,(x,y,z,r))
data.append([x,y,z,r,temp])
f.close()
return data
def show_dock_spheres(filename,transparency=0.40):
Reads in a DOCK sphere file and graphs the
results as dock spheres. You can pass the
transparency as an additional argument.
transparency = float(transparency)
data = dock_file_to_data(filename)
graph_temp_via_cgo('dock_spheres',data,transparency)
cmd.extend('sds',show_dock_spheres)
On 4/6/07, DeLano Scientific del...@delsci.info wrote:
Pre 1.0:
fragment methane, mysph
remove hydro and mysph
alter mysph, vdw=2.0
as spheres, mysph
set sphere_transparency, 0.5, mysph
Post 1.0:
pseudoatom mysph, vdw=2.0
as spheres, mysph
set sphere_transparency, 0.5, mysph
Cheers,
Warren
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On
Behalf Of jjv5
Sent: Friday, April 06, 2007 4:55 AM
To: PyMOL-users@lists.sourceforge.net
Subject: [PyMOL] Single transparent sphere
Hi,
Does anyone know of a good way to create a single transparent sphere of
varying size? We've tried using a single atom and changing the vdw, but we
are unable to produce a surface of a single atom. CGO objects work but
cannot be made transparent. What we'd really like is a transparent CGO
sphere. Any ideas?
Thanks,
Jim
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Re: [PyMOL] APBS surface
PyMOL doesn't know where the electrostatic potential map comes from. If you load up a map and a structure, it will show the potential from that map on that structure. On 4/2/07, Gianluigi Caltabiano chimic...@yahoo.it wrote: YesI have already done as wrote My question iswhat if I up load ligand surface with receptor structure? Will it, as I think, shows me the potential of ligand on the receptor surface (giving me as sort of negative of ligand surface on receptor's)??? Thank for your answer, Gianluigi Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain - Messaggio originale - Da: Mike Summers summ...@hhmi.umbc.edu A: Gianluigi Caltabiano chimic...@yahoo.it Inviato: Martedì 27 marzo 2007, 20:14:37 Oggetto: Re: [PyMOL] APBS surface You need to create individual proteins and then create maps for the individual protein; e.g, create A,(structure and residues_of_A_only) Mike On Tue, Mar 27, 2007 at 01:35:56PM +, Gianluigi Caltabiano wrote: Hi everyone, I am working with a protein-protein complex and I have calculated for each protein, let's say A and B, apbs electrostatic surfaces. Everything works fine. My question is: I have uploaded the structure of protein A and the surface of protein B. What it shows to me is a blank surface for most of the protein A but the part where protein B interact whit it. I think, but I would have confimations, that I am, in some way, projecting potential values of protein's surface B on the surface of protein A, like having a negative of the B interactions. It seems it works like this since I know both rotein's interacting residues and now I am facing interacting patch of residues from protein B on their counnter part on protein A. Am I wrong? Thank for your answer, in advance, Gianluigi Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain ___ L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail: http://it.docs.yahoo.com/nowyoucan.html - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- * Michael F. Summers Department of Chemistry and Biochemistry and Howard Hughes Medical Institute University of Maryland Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 Phone: (410)-455-2527 FAX: (410)-455-1174 Email: summ...@hhmi.umbc.edu Web: www.hhmi.umbc.edu L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net
Re: [PyMOL] Electrostatic surface visualization
On 3/3/07, se...@uniroma2.it se...@uniroma2.it wrote: Dear all, I'm new to this list and to the software. I used PyMOL and APBS to calculate an electrostatic surface for a small protein (I'm using the WindowsXP version) and everything seems fine. Now I would like to visualize this surface AND the secondary structure of the protein, in order to understand the positive and negative regions. How I can do? Some software show the surface in trasparency but it seems this is not possible in PyMOL. You can do this with commands like set transparency, 0.5, myproteinname or set transparency, 0.2, iso_pos A related question: it is possible to color the secondary structure according to the electrostatic surface properties? I have an NMR titration of this protein with its partner: I would like to relate the shifts of the NH backbone with the electrostatic surface. Not sure about that one. -Michael I looked at the archive but I haven't found an answer. Thanks in advance, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, Tor Vergata via della Ricerca Scientifica, 00133, Rome, Italy e-mail:se...@uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328 - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net
Re: [PyMOL] reload modified wizard
I found an old version of my code. It was just slightly more
complicated than I thought. Here's a version of the wrapper that I
was using:
import sys
sys.path.append('/home/mlerner/work/src/PyMOL_Plugins/')
import SomethingOrOtherTools
def __init__(self):
self.menuBar.addmenuitem('Plugin', 'command',
'SomethingOrOther',
label='SomethingOrOther...',
command = lambda s=self:
getSomethingOrOtherTools(s))
def getSomethingOrOtherTools(thing):
reload(SomethingOrOtherTools)
return SomethingOrOtherTools.SomethingOrOtherTools(thing)
Let me know if you have any more questions.
-michael
On 2/24/07, Michael Lerner mgler...@gmail.com wrote:
Actually, I did this when I was developing the APBS Plugin. I put all
of the interesting code in a module called _apbs_tools. apbs_tools
was just a little wrapper where the init function would import and
reload _apbs_tools and then call through to it.
-Michael
On 2/24/07, DeLano Scientific del...@delsci.info wrote:
I believe this is a limitation of Python: once a code module is loaded and
initialized, it is difficult to reload it...you might be able to hack it
though.
-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf
Of bgbg bg
Sent: Saturday, February 24, 2007 5:19 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] reload modified wizard
Hello,
I develop several custom PyMol wizards. Is there any way to
reload a modified wizard, without restarting PyMol?
Thank you.
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--
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner http://lernerclan.net
Re: [PyMOL] reload modified wizard
Actually, I did this when I was developing the APBS Plugin. I put all of the interesting code in a module called _apbs_tools. apbs_tools was just a little wrapper where the init function would import and reload _apbs_tools and then call through to it. -Michael On 2/24/07, DeLano Scientific del...@delsci.info wrote: I believe this is a limitation of Python: once a code module is loaded and initialized, it is difficult to reload it...you might be able to hack it though. -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of bgbg bg Sent: Saturday, February 24, 2007 5:19 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] reload modified wizard Hello, I develop several custom PyMol wizards. Is there any way to reload a modified wizard, without restarting PyMol? Thank you. -- --- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforge CID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net
Re: [PyMOL] Visualizing Molecular Orbitals in PyMol
Hi, I don't remember the details, but I do remember that I had some troubles using bricks when I was writing the APBS plugin. The DX file format is really simple, though, especially for this sort of thing. http://apbs.sourceforge.net/doc/user-guide/index.html#opendx-format If I recall correctly, my problems with bricks were mostly that I wasn't using them correctly, but I didn't figure out how to use them correctly until after I'd already converted everything to DX. -Michael Lerner On 2/19/07, BuzB bmb...@gmail.com wrote: Hi All, Thanks to everyone and for the responses to and encouragement about my query on visualizing molecular orbitals in pymol. I'm using PyMol 0.99rc6. I feel like I'm quite close to a solution. I've developed a routine to compute a 3 dimensional matrix containing the probability amplitudes of the orbitals, which I can load into a PyMol brick object. Then, things start to go wrong When I use the load_brick function in the cmd module; cmd.load_brick(brik, Brick) or alternatively, cmd.load_object(loadable.brick, brik, Brik) PyMol returns the message; ObjectMap: Map Read. Range = 0.000 to 0.000 but it does display the object Brick in the objects menu. I can then create an isomesh or surface with the command; cmd.isosurface(BrikSurf, Brick, 0.1) But no surface is displayed on screen. The example file brick01.py that is included in examples/devel does something almost identical to what I'm trying to do, it displays an exponentially decaying density, but also with no success in PyMol 0.99rc6. Is there a bug somewhere in the load_brick function that I'm running into? Thanks a lot! bmb197 - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net
Re: [PyMOL] Side by side views
Warren helped me with a similar problem a while ago (I can't find the link in the mailing list archive), and this might do the job for you: If you download and run my script at http://www-personal.umich.edu/~mlerner/Pymol/mg_pymol_utils.py you can start up two PyMOL sessions. You then type send_view in one of them, receive_view in the other one, and the receive_view one will follow along. I don't know how to get that all working in one window, but you can always just paste the images together. I find this really useful for comparing structures with different ligands bound, different parts of a dynamics run, etc. In your case, you might need to align all of the structures to one reference structure first, so that the views are similar. Hope this helps, -Michael Lerner On 25 Jan 2007 16:32:21 +, David F Burke df...@cam.ac.uk wrote: Pymol users, I wish to compare several protein structures and was wondering how or if, in pymol, one can view two structures side by side and rotate each structure around their own centre of gravity. This is a bit like stereo view but with different structures in the left and right views. Many thanks David -- David Burke PhD Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ Email:df...@cam.ac.uk Tel: 01223 330933 - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net
Re: [PyMOL] New plugin and Doubt with APBS Tools
We discussed this a bit off-list, and it looks like this was the answer: The potentials are assigned to points in space. That's why the isosurfaces don't change, and also why the surface coloring changes when you change the shape of the surface. Hope that helps anyone else who might have this question, -michael On 1/9/07, Michael Lerner mgler...@gmail.com wrote: Raúl, I don't have time to look at this in detail right now, but .. what exactly do you mean that the potentials change between frames? What happens if you draw isosurfaces? Do they change? -michael On 1/7/07, Raúl Mera butil_li...@yahoo.com wrote: Dear all, Two things. First, I just written a small plugin that uses the program reduce to add hydrogens to a molecule or to a trajectory loaded in Pymol.(since each frame of the trajectory is hydrogenated by reduce, I think that protonation states could vary between frames) This allow us to have a reliable protonation method in PyMOL, without having to save the structure as PDB and hydrogenate with another app, and using an open-source (as far as I know) and easy to install application. Since I don't have any website right now, I will try to make it available from the Pymol Wiki. If you want the plugin right now, just e-mail me. The other thing is a doubt in using the APBS Tools. When I use it to calculate electrostatics potentialsof a trajectory (but the PQR is made by PDB2PQR from a PDB made with PyMOL, i.e, only from the first snapshot) I get a .dx map that I think has the potentials only for the first frame. When I display the potential surface in the trajectory, the potentials seems to change between frames, which I wouldn't expect since I think that the calculation was performed only for the first frame. My doubt is: Are these changes alleatory due to a change of the structure's position changes on the grid, or they have some significance?, if the latter, what significance? (maybe the changes are produced by the motion of polar groups?) Thanks in advance, Raul __ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ¡gratis! Regístrate ya - http://correo.espanol.yahoo.com/ - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net
Re: [PyMOL] New plugin and Doubt with APBS Tools
Raúl, I don't have time to look at this in detail right now, but .. what exactly do you mean that the potentials change between frames? What happens if you draw isosurfaces? Do they change? -michael On 1/7/07, Raúl Mera butil_li...@yahoo.com wrote: Dear all, Two things. First, I just written a small plugin that uses the program reduce to add hydrogens to a molecule or to a trajectory loaded in Pymol.(since each frame of the trajectory is hydrogenated by reduce, I think that protonation states could vary between frames) This allow us to have a reliable protonation method in PyMOL, without having to save the structure as PDB and hydrogenate with another app, and using an open-source (as far as I know) and easy to install application. Since I don't have any website right now, I will try to make it available from the Pymol Wiki. If you want the plugin right now, just e-mail me. The other thing is a doubt in using the APBS Tools. When I use it to calculate electrostatics potentialsof a trajectory (but the PQR is made by PDB2PQR from a PDB made with PyMOL, i.e, only from the first snapshot) I get a .dx map that I think has the potentials only for the first frame. When I display the potential surface in the trajectory, the potentials seems to change between frames, which I wouldn't expect since I think that the calculation was performed only for the first frame. My doubt is: Are these changes alleatory due to a change of the structure's position changes on the grid, or they have some significance?, if the latter, what significance? (maybe the changes are produced by the motion of polar groups?) Thanks in advance, Raul __ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ¡gratis! Regístrate ya - http://correo.espanol.yahoo.com/ - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net
[PyMOL] Showing the surface
Hi, I want to show the electrostatic potential surface 10A away from a protein. I used to do this by setting all of the vdw radii to 10A, but I'm wondering if there's a better way these days. The surface I got by altering the vdw radii always looked really choppy and not so smooth. Thank you, -Michael Lerner -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net
Re: [PyMOL] Paths to loaded objects
I think he means for you to have a Load button as part of your plugin. That button would first record the path to the file and then call through to cmd.load(). On 8/19/06, Ron Jacak r...@email.unc.edu wrote: Peter, I'm working on a plugin that reads information appended to the end of PDB files to draw CGO objects. Right now, I have the user specify the filesystem path to the currently loaded objects through the plugin GUI so that I know where to go to find the file. For one object, this isn't so bad. But if users load multiple objects that are in different directories, I will have to change the GUI so that the user has to specify the path to each object loaded. This kind of situation would quickly become tedious. Does PyMOL store the paths for objects that are loaded somewhere? I know I can get the current working directory using getcwd(), so I'm hoping there's a way to get the path to the loaded objects as well. I don't know of a way to get file information from a pymol object, but you could work around this by using a python dictionary (when the pdb file is loaded, store the full path to the file in a dictionary using the pymol object name as the key). I'm not sure I fully understand your suggestion. It sounds to me like what you're saying is that I should add code (e.g. a dictionary) to the importing.py load() function which saves the file information of objects as they're loaded. But then instead of just distributing my plugin, I would have to get users to change their PyMOL source, as well (which I'm not willing to do). Am I understanding correctly? Any other ways around this problem? -Ron Ron Jacak Graduate Student University of North Carolina - Chapel Hill - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] rejected atoms during alignment
This is not a great answer, but do you know about the object parameter for the align command? I often type something like align struct1, struct2, object=alignment and then just look at which things were included/excluded. -michael On 8/3/06, Marc Bruning brun...@mpghdb.desy.de wrote: hello, is there any way to find out which atoms are discarded during the refinement cycles of the align command? regards, marc - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] How do I show multiple conformations in a single crystal structure?
I have a crystal structure that contains two conformations for a flexible loop. They're both in the crystal structure, but have occupancies less than one. When I look at the structure in PyMOL, I see only one conformation. Is there a command similar to split_states that will allow me to view both conformations at once? Thanks, -michael
Re: [PyMOL] How do I show multiple conformations in a single crystal structure?
Oh, if it helps, the residues are all named things like ACYS and BCYS for the different conformations. On 7/25/06, Michael Lerner mgler...@gmail.com wrote: I have a crystal structure that contains two conformations for a flexible loop. They're both in the crystal structure, but have occupancies less than one. When I look at the structure in PyMOL, I see only one conformation. Is there a command similar to split_states that will allow me to view both conformations at once? Thanks, -michael
[PyMOL] Can PyMOL read amber8 trajectory files?
I have some stuff from an amber8 (sander) MD run that I'd like to visualize in PyMOL. When I load it up, PyMOL says something like assuming amber6 format and dies. I'm using fink/pymol-py24 on an intel macbook pro. I always forget how to load amber files anyway, so I could easily be screwing something up. I call my topology file something.top and here's what happens: PyMOLload something.top ObjectMolecule: Assuming this is an Amber6 topology file. TOPStrToCoordSet-Error: Error reading atom types /sw/bin/pymol: line23:Bus error I made that file with amber8. Thanks, -michael
Re: [PyMOL] why is PyMOL renaming my residues?
Hi Warren, PyMOL's PDB handling is an attempt to navigate a minefield of incompatible standards which exist in the conventions of various software packages. Ugh. I know more about incompatable PDB files than I ever wanted to. I once wrote something much like Andrew Dalke's UPDB (see http://biopython.org/scriptcentral/). Unfortunately, my version ended up being very slow, so I didn't get a chance to give it to the biopython folks. I keep meaning to go back and speed it up, but I think they have a good PDB parser now. Since version 0.90, PyMOL's behavior has changed. Nowadays, your input data: snip Would be returned as: snip ...which does preserve atom names, but not the order. Note that white-space in the atom names is not preserved (an inherent limitation in PyMOL -- significant white-space within identifier is hell on users and parsers). Conventionally, atom names of length 3 or less are placed in the second column, not the first -- so your LMN atom may cause trouble. That's fine with me. I just had LMN and XYZ in there so that I could figure out exactly what PyMOL was changing. Also note that by some conventions, 2OA2 in a PDB file really means atom OA22. I didn't know that. What conventions are those? Furthermore, in your example, they [ATOM IDs] are not unique (a mistake?). yup, a mistake. However, I am trying to bend PyMOL around to meet your needs a bit better. Towards this end, I've created a new setting pdb_retain_ids which preserves the original PDB serial numbers in the output file. In future PyMOL versions, so long as set retain_order, 1 set pdb_retain_ids, 1 set pdb_no_end_record, 1 That's absolutely fantastic. Right now, I have to use PyMOL, MOE and AMBER (sander and carnal are the real problems) on the same systems, and anything that makes this less painful is great! I'll probably set retain_order and pdb_retain_ids in my .pymolrc.py and upgrade to the CVS version within the next couple of days. Thanks! -michael -- michael lerner
[PyMOL] why is PyMOL renaming my residues?
Hi, If I load up a PDB file that looks like this: HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 31.54 O HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 21.05 O HETATM 1314 ABCD NAP 164 28.554 64.174 16.275 11.05 O HETATM 1314 XYZ NAP 164 30.554 66.174 18.275 1.05 O HETATM 1314 LMN NAP 164 32.554 68.174 20.275 41.05 O and then save it from PyMOL, the resulting PDB file looks like this: HETATM1 2OA2 NAP 164 28.315 61.969 12.250 0.00 31.54 O HETATM2 3OA2 NAP 164 26.554 62.174 14.275 0.00 21.05 O HETATM3 DABC NAP 164 28.554 64.174 16.275 0.00 11.05 O HETATM4 LMN NAP 164 32.554 68.174 20.275 0.00 41.05 O HETATM5 XYZ NAP 164 30.554 66.174 18.275 0.00 1.05 O END You'll note that OA22 has been renamed to 2OA2, OA23 has been renamed to 3OA2 and ABCD has been renamed to DABC. It looks to me like residue with a four-letter name is getting renamed. No .. wait .. it's a little stranger than that .. if I open up the second file (the one with DABC) and save *it*, I get this: HETATM1 2OA2 NAP 164 28.315 61.969 12.250 0.00 31.54 O HETATM2 3OA2 NAP 164 26.554 62.174 14.275 0.00 21.05 O HETATM3 CDAB NAP 164 28.554 64.174 16.275 0.00 11.05 O HETATM4 LMN NAP 164 32.554 68.174 20.275 0.00 41.05 O HETATM5 XYZ NAP 164 30.554 66.174 18.275 0.00 1.05 O END Note that ABCD went to DABC which went to CDAB, but OA22 went to 2OA2 and stayed there. LMN and XYZ weren't touched. Is there a way to supress this behavior? It causes me a bit of trouble when, e.g., my AMBER parameter files expect residues to have certain names. I'm not sure exactly when PyMOL decides to rename things .. if I shift-left-click on one of the residues in the first file (either before or after saving), PyMOL says You clicked NAP: /test1///164/OA23 (i.e. it gives me the original name). thanks, -michael -- michael lerner
[PyMOL] Re: why is PyMOL renaming my residues?
oops .. two problems with my last message: 1) i said residue a few times when i meant atom .. it should be obvious from the context of the message. 2) my email program seems to have messed up some of the formatting in the last message .. the original PDB file should look like this (assuming i can format it correctly this time): HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 31.54 O HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 21.05 O HETATM 1314 ABCD NAP 164 28.554 64.174 16.275 11.05 O HETATM 1314 XYZ NAP 164 30.554 66.174 18.275 1.05 O HETATM 1314 LMN NAP 164 32.554 68.174 20.275 41.05 O in case that's still not formatted correctly, each line should begin with HETATM, and the point is that the atoms are named OA22, OA23, ABCD, XYZ and LMN respectively. also, i noticed that PyMOL is changing the atom ID (OA22 was 1313 in the first file, but 1 in the second). that's not actually causing me any trouble, but i'm curious: is there a way to make PyMOL leave the IDs alone? thanks, -michael michael lerner wrote: Hi, If I load up a PDB file that looks like this: HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 31.54 O HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 21.05 O HETATM 1314 ABCD NAP 164 28.554 64.174 16.275 11.05 O HETATM 1314 XYZ NAP 164 30.554 66.174 18.2751.05 O HETATM 1314 LMN NAP 164 32.554 68.174 20.275 41.05 O and then save it from PyMOL, the resulting PDB file looks like this: HETATM1 2OA2 NAP 164 28.315 61.969 12.250 0.00 31.54 O HETATM2 3OA2 NAP 164 26.554 62.174 14.275 0.00 21.05 O HETATM3 DABC NAP 164 28.554 64.174 16.275 0.00 11.05 O HETATM4 LMN NAP 164 32.554 68.174 20.275 0.00 41.05 O HETATM5 XYZ NAP 164 30.554 66.174 18.275 0.00 1.05 O END You'll note that OA22 has been renamed to 2OA2, OA23 has been renamed to 3OA2 and ABCD has been renamed to DABC. It looks to me like residue with a four-letter name is getting renamed. No .. wait .. it's a little stranger than that .. if I open up the second file (the one with DABC) and save *it*, I get this: HETATM1 2OA2 NAP 164 28.315 61.969 12.250 0.00 31.54 O HETATM2 3OA2 NAP 164 26.554 62.174 14.275 0.00 21.05 O HETATM3 CDAB NAP 164 28.554 64.174 16.275 0.00 11.05 O HETATM4 LMN NAP 164 32.554 68.174 20.275 0.00 41.05 O HETATM5 XYZ NAP 164 30.554 66.174 18.275 0.00 1.05 O END Note that ABCD went to DABC which went to CDAB, but OA22 went to 2OA2 and stayed there. LMN and XYZ weren't touched. Is there a way to supress this behavior? It causes me a bit of trouble when, e.g., my AMBER parameter files expect residues to have certain names. I'm not sure exactly when PyMOL decides to rename things .. if I shift-left-click on one of the residues in the first file (either before or after saving), PyMOL says You clicked NAP: /test1///164/OA23 (i.e. it gives me the original name). thanks, -michael -- michael lerner
