Hi Daniel, the "bymol" (long: bymolecule, short: bm.) operator expands the selection to complete molecules, so all atoms which are connected by bonds. This is independant of atomic identifiers, unlike the "byres" operator.
http://www.pymolwiki.org/index.php/Selection_Algebra The ID rolling problem is a problem of the PDB file format. The load_gro function in PSICO (http://pymolwiki.org/index.php/Psico) for example does some tricks to read in ID and resi numbers beyond the PDB limitation. Cheers, Thomas Daniel Mann wrote, On 07/05/13 14:09: > Hey Thomas, > could you elaborate on the "bymol" flag? E.g. the given example of > selecting molecules when you got > 9999 waters? Is there an easy > workaround for the ID rolling? > > Regards, > Daniel > > Am 01.07.13 21:38, schrieb Thomas Holder: >> Matthew Baumgartner wrote, On 07/01/13 21:34: >>> I removed the byres command because I have more then 10000 water >>> molecules in my system and the residue ID's were rolling over and waters >>> far from the residue of interest were being selected. >>> If anyone has a suggestion on this, please let me know, I would like to >>> select whole water molecules for making figures. >> use "bymol". >> >> Cheers, >> Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev _______________________________________________ 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
