From: Stephanie E. <sendsley@u.washington.edu> - 2005-05-18 22:37:36
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Hi there, I can get MacPyMol to find distances between a ligand and protein, but I want to output a list of all of these distances. I have looked everywhere on how to do this, and I saw another posting with the same question, but it wasn't answered. Does anyone out there know how to get a list of the distances that PyMol calculates? Please help. Thanks Steph |
From: Warren D. <wa...@de...> - 2005-05-19 00:36:05
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Stephanie, This is a very reasonable request, but unfortunately it is not one that PyMOL can meet at present -- it will require some significant changes within the C code for the "distance" command. Thank you for the suggestion. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of > Stephanie Endsley > Sent: Wednesday, May 18, 2005 3:38 PM > To: pym...@li... > Subject: [PyMOL] listing distance measurements > > Hi there, > > I can get MacPyMol to find distances between a ligand and > protein, but I want to output a list of all of these > distances. I have looked everywhere on how to do this, and I > saw another posting with the same question, but it wasn't answered. > > Does anyone out there know how to get a list of the distances > that PyMol calculates? Please help. > > Thanks > > Steph > > > > ------------------------------------------------------- > This SF.Net email is sponsored by Oracle Space Sweepstakes > Want to be the first software developer in space? > Enter now for the Oracle Space Sweepstakes! > http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Dan K. <dw...@bi...> - 2005-05-19 13:50:07
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Maybe I'm understanding the question wrong, but here is a solution for getting a list of all atom-atom distances between a ligand and a protein. Just change the pdb id, and the definitions of the protein and ligand to your case. A list of these distances will then be in the dist_list object, which you can do anything you want with. In the example I simply printed them out. To run example below (if saved as distlist.py) from pymol: run distlist.py ~ Dan --- Dan Kulp Biophysics Graduate Student @ UPenn dw...@ma... http://dwkulp.homelinux.net/tiki/tiki-index.php --- ------------------------------------------------------------ import cmd cmd.load("1O2K.pdb") cmd.select("protein","not resn 656 and not resn HOH") cmd.select("ligand", "resn 656") dist_list = {} pro_atoms = cmd.get_model("protein") lig_atoms = cmd.get_model("ligand") for l_at in lig_atoms.atom: for p_at in pro_atoms.atom: dist_list[str(l_at.resi)+":"+l_at.name+";"+str(p_at.resi)+":"+p_at.name] = cmd.dist("foo", "index "+str(l_at.index),"index "+str(p_at.index)) cmd.delete("foo") print "LIST OF ATOM-ATOM PROTEIN-LIGAND DISTANCES" for d in dist_list.keys(): print "Distance of "+d+" is "+str(dist_list[d]) ---------------------------------------------------------- Warren DeLano wrote: >Stephanie, > >This is a very reasonable request, but unfortunately it is not one that >PyMOL can meet at present -- it will require some significant changes >within the C code for the "distance" command. > >Thank you for the suggestion. > >Cheers, >Warren > >-- >Warren L. DeLano, Ph.D. >Principal Scientist > >. DeLano Scientific LLC >. 400 Oyster Point Blvd., Suite 213 >. South San Francisco, CA 94080 USA >. Biz:(650)-872-0942 Tech:(650)-872-0834 >. Fax:(650)-872-0273 Cell:(650)-346-1154 >. mailto:wa...@de... > > > > >>-----Original Message----- >>From: pym...@li... >>[mailto:pym...@li...] On Behalf Of >>Stephanie Endsley >>Sent: Wednesday, May 18, 2005 3:38 PM >>To: pym...@li... >>Subject: [PyMOL] listing distance measurements >> >>Hi there, >> >>I can get MacPyMol to find distances between a ligand and >>protein, but I want to output a list of all of these >>distances. I have looked everywhere on how to do this, and I >>saw another posting with the same question, but it wasn't answered. >> >>Does anyone out there know how to get a list of the distances >>that PyMol calculates? Please help. >> >>Thanks >> >>Steph >> >> >> >>------------------------------------------------------- >>This SF.Net email is sponsored by Oracle Space Sweepstakes >>Want to be the first software developer in space? >>Enter now for the Oracle Space Sweepstakes! >>http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click >>_______________________________________________ >>PyMOL-users mailing list >>PyM...@li... >>https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> >> > > > > >------------------------------------------------------- >This SF.Net email is sponsored by Oracle Space Sweepstakes >Want to be the first software developer in space? >Enter now for the Oracle Space Sweepstakes! >http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click >_______________________________________________ >PyMOL-users mailing list >PyM...@li... >https://lists.sourceforge.net/lists/listinfo/pymol-users > > > |
From: Marc B. <br...@mp...> - 2005-05-23 10:28:32
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dear list, is it possible to distribute the pymol gui and the viewer between different display variables, say the gui to "display:0.0" and the viewer to "display:0.1"? regards, marc bruning |