Hi Roger, On 09 Apr 2014, at 14:55, Roger Rowlett <rrowl...@colgate.edu> wrote: > [...] I don't know how sophisticated PyMols morphing command is, but some > morphing programs simply do a linear interpolation between the starting and > ending states, and that will lead to serious distortion of side chain and > main chain geometries. The CNS morphing script will sort these out. [...]
PyMOL (or RigiMOL, which actually does the morphing job) is quite sophisticated, it analyses the two structures for hinge regions and tries to rotate rigid parts around those hinge regions. That first step might produce distorted side chain conformations, which is then sorted out in the subsequent refinement procedure. That refinement just aims to maintain the local geometry (bond length and angles of side chains) of start and end conformation through the morph. Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test & Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees _______________________________________________ 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
