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 (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
