From: Joel T. <joe...@ot...> - 2012-05-09 03:14:28
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Hi folks, So I have no scripting skills in python but I can use pymol reasonably well. I want to superimpose (pair_fit) 4 atoms (all the same) from a library of conformers onto a template molecule (similar to clustering after conformational searching). I could probably nut out how to do the pairfitting actually I could do this easily by command line but I have > 100 molecules so I'm not sure how to script this. Any help would be welcome Cheers Joel _________________________________ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293 |
From: Troels E. L. <tl...@gm...> - 2012-05-09 07:18:13
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If you have some name scheme for your molecules, you could figure it out from this: You want to make a python block: python .... do python code here python end Then define a loop, and figure out to call your naming scheme. Do a calculation, and add the result to an array or something. reinitializeimport propkacmd.bg_color("white")cmd.set("auto_zoom","off") results = [] python resis = [["1DSB","*","30"],["1ERT","*","32"]] for p,c,r in resis: cmd.fetch(p,async="0") cmd.refresh() pkavalues = propka.propka(molecule=p,chain=c,resi=r,logtime="",makebonds="no") results.append(pkavalues) cmd.refresh() python end 2012/5/9 Joel Tyndall <joe...@ot...> > Hi folks,**** > > ** ** > > So I have no scripting skills in python but I can use pymol reasonably > well. **** > > ** ** > > I want to superimpose (pair_fit) 4 atoms (all the same) from a library of > conformers onto a template molecule (similar to clustering after > conformational searching). I could probably nut out how to do the > pairfitting actually I could do this easily by command line but I have > > 100 molecules so I’m not sure how to script this.**** > > ** ** > > Any help would be welcome**** > > ** ** > > Cheers**** > > > Joel**** > > ** ** > > _________________________________**** > > Joel Tyndall, PhD > > Senior Lecturer in Medicinal Chemistry > National School of Pharmacy > University of Otago > PO Box 56 Dunedin 9054 > New Zealand **** > > Skype: jtyndall**** > > ** ** > > Ph: +64 3 479 7293**** > > ** ** > > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
From: Thomas H. <sp...@us...> - 2012-05-10 08:05:27
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Hi Joel, there are several ways how this could be done. Are those conformers all the same molecule (identical identifiers and topology)? Then you can load them into a multi-state object and use intra_fit on the selection of the four atoms. This will fit all to state 1. If you have the "psico" module installed, you can use extra_fit which is similar to the first solution, but for individual objects. Example: # fetch some triphosphates from pubchem load http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=6830&disopt=3DSaveSDF, template, format=sdf load http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=454448&disopt=3DSaveSDF, format=sdf load http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=45102407&disopt=3DSaveSDF, format=sdf # superimpose on phosphate atoms extra_fit elem P Third solution was already proposed by Troels. Use a python loop in combination with any of cmd.align, cmd.fit or cmd.pair_fit, Example: python for obj in cmd.get_object_list(): cmd.pair_fit(obj + ' and elem P', 'template and elem P') python end Hope that helps. Cheers, Thomas On 05/09/2012 05:14 AM, Joel Tyndall wrote: > Hi folks, > > So I have no scripting skills in python but I can use pymol reasonably > well. > > I want to superimpose (pair_fit) 4 atoms (all the same) from a library > of conformers onto a template molecule (similar to clustering after > conformational searching). I could probably nut out how to do the > pairfitting actually I could do this easily by command line but I have > > 100 molecules so I’m not sure how to script this. > > Any help would be welcome > > Cheers > > Joel > _________________________________ > > Joel Tyndall, PhD > > Senior Lecturer in Medicinal Chemistry > National School of Pharmacy > University of Otago > PO Box 56 Dunedin 9054 > New Zealand > > Skype: jtyndall > > Ph: +64 3 479 7293 -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |