Hi John, Does the 'torsion' command work?
Cheers, Doug Quoting johnbax...@cs.unm.edu on Thu, 20 Nov 2014 01:06:04 -0700: > Hello, PyMOL users! > > I am trying to figure out within the Python interface how to rotate the > parts of a molecule on one side of a bond about that bond's axis, given > only the two atoms defining the bond and a angle to rotate by (that is, > without requiring me to specify four atoms and a final dihedral angle > value as required by set_dihedral). While I understand the "rotate" > function, I can't figure out how, in the Python interface, to select the > atoms on one side of a bond given the bond's two defining atoms. > > I've looked through the PyMOL C++ code, and it appears that this > functionality is provided by the layer3/Selector.cpp function > "SelectorSubdivide" when its "bondMode" flag set to true and given two > atoms; set_dihedral's C++ implementation seems to use this functionality > to select the atoms it will rotate. I tried to look through the rest of > the source to see if this selection behavior was somehow exposed to the > Python interface, but as best as I could tell it doesn't seem to be. > > If anyone can work out a good way from the Python interface to select the > atoms of a molecule on one side of a bond, or if there is a > Python-accessible function that acts similar to set_dihedral but rotates > about any bond by a given angular change without requiring a bonded > sequence of four atoms to define an arbitrary dihedral plane (and an > otherwise unnecessary call to get_dihedral to to calculate the change > needed to know what angle I would need to give set_dihedral), I would be > very appreciative. > > Thank you very much for your time! > > -John > > > ------------------------------------------------------------------------------ > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server > from Actuate! Instantly Supercharge Your Business Reports and Dashboards > with Interactivity, Sharing, Native Excel Exports, App Integration & more > Get technology previously reserved for billion-dollar corporations, FREE > http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk > _______________________________________________ > 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 > > _____________________________________________________ Dr. Douglas R. Houston Lecturer Institute of Structural and Molecular Biology Room 3.23, Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 http://tinyurl.com/douglasrhouston -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk _______________________________________________ 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
