Hi Martin, I think it would be good to use pair_fit
Someone else may be able to help with a scdropt buut if you have a stretch of residues you can align them such as: Pair_fit a///79-85/ca, b///89-95 , a///150-175/ca, b///183-208/ca (this aligns a to b) You could also renumber chain A to match the numbers of chain B (if it doesn't already match) I'm pretty sure this will give you what you want. It is at least one method 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 http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 -----Original Message----- From: Martin Hediger [mailto:[email protected]] Sent: Thursday, 25 March 2010 10:51 p.m. To: [email protected] Subject: [PyMOL] Align different Structures Hi all, My problem is: I have two structures, A and B. Both are part of a protein and contain residues from the active site. A is a subset of B in a sense that B is contains residues even further from the active site (generated by the expand command). I ran a QM calculation on the active site in the minimal set A to obtain a transition state for an enzymatic reaction (ester cleavage). So A is not in its original configuration anymore, i.e. some of the residues have moved. What I want to do is this: the same calculation on the expanded model B would be too expensive. So I want to align B as reasonably as possible to A, since I know what the transition state looks like in the simple model. How do I do this in the smartest way? By pair-fitting in Pymol? I believe to issue the align command is not the best idea, since i dont want an overlay, I want the catalytically relevant residues to be superimposed. I would very much appreciate any suggestions. Martin ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected] ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
