If you have access to the incentive version, I would recommend looking at the new properties capabilities in Pymol. The distances can be nicely encoded in a property and rendered with spectrum w/o having to resort to messing with other properties like B-factors. I believe the docs at Schrodinger contain examples to that end.
HTH Carsten From: David Hall [mailto:li...@cowsandmilk.net] Sent: Wednesday, November 18, 2015 8:13 AM To: Smith Liu Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] on coloring residues based on y values in the x y z coordinates I forgot: spectrum b at the end. On Wed, Nov 18, 2015 at 8:11 AM, David Hall <li...@cowsandmilk.net<mailto:li...@cowsandmilk.net>> wrote: Assuming you are ok with overwriting the B-factors stored.y=[] iterate_state 1, prot, stored.y.append(y) % prot here should be replaced with your pymol object name alter prot, b=stored.y.pop(0) % again, replace prot with your pymol object name On Wed, Nov 18, 2015 at 7:49 AM, Smith Liu <smith_liu...@163.com<mailto:smith_liu...@163.com>> wrote: Dear All, Is any way we can colour the molecule by pymol based on the y values in the z y z coordinates, so that we can view easily the residues (or atoms) with equivalent position in the primary sequence but has a y-axis shift in the 3-D structure? Smith ------------------------------------------------------------------------------ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto: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
------------------------------------------------------------------------------
_______________________________________________ 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
