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 ------------------------------------------------------------------------------ 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
