Hi Tom, There is the "connect_cutoff" setting, see https://pymolwiki.org/index.php/connect_cutoff
The bonds do not affect residue numbers in PyMOL, those should be unchanged and identical to your original input file. Cheers, Thomas On 03 Jan 2017, at 07:07, Thomas Charles Pochapsky <pocha...@brandeis.edu> wrote: > Hi, I exported a PDB file from PyMOL that includes explicit water from a > dynamics track. However, many of the solvent molecules are either > doubled (same residue number for two different waters) or truncated > (missing a hydrogen, or a hydrogen given a separate residue number). I > am assuming that PyMOL assigns bonds based on distance between atoms, is > there a way to minimize this? The RCSB doesn't like my current PDB file! > > Thanks, Tom Pochapsky -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ 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
