Hi Wei, Is this an ensemble of docking poses all overlayed in the same PDB file, and not separated by MODEL records? PyMOL does distance based bonding when loading data from PDB files. Which docking program generated this file?
Cheers, Thomas > On Jul 9, 2018, at 4:57 PM, Wei Song <weisong...@gmail.com> wrote: > > Hello, > > I got a structure (attached figure) of a lipid after docking it with a > protein. The original structure before the docking is in SDF file, not > regular PDB. I've never seen a docked structure like this with many of the > atoms having more bonds than they actually can have like some carbons (blue) > are having five even six bonds in the display, and the whole molecule looks > like a plate. Is there anyone who also have met this problem before or any > idea to get the structure back normal display. > > Thank you and I appreciate any suggestions and ideas. > > Best, > Wei > <UNADJUSTEDNONRAW_thumb_f09.jpg> -- 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
