Re: [PyMOL] Atoms forming more bonds than they should have
Hi Thomas, This is a single docking poses produced by Autodock Vina. I did get several poses, but all of them look similar and a flat structure. I am thinking of that this might be due to the 2D (not 3D) structure of the lipid which I used for protein docking as I was not able to get a 3D for this lipid. And I am still trying to convert the 2D structure to a reliable 3D one. Thanks, Wei On Tue, Jul 10, 2018 at 4:49 AM Thomas Holder wrote: > 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 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 > > > > -- > 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
Re: [PyMOL] Atoms forming more bonds than they should have
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 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 > -- 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
[PyMOL] Atoms forming more bonds than they should have
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 [image: UNADJUSTEDNONRAW_thumb_f09.jpg] -- 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
