Hi Fred, At least Schrodinder's PyMOL 2.3.2 can open Vina's PDBQR files (with multiple docked conformations) without any problems or additional CIFs in my experience. Different conformations of ligands are loaded as different states.
It if is an older version you could try to convert Vina's PDBQR to PDB: 1. Split PDBQT file (vina_split comes together with Vina): vina_split --input file.pdbqt 2. Convert PDBQT to PDB: cut -c-66 file_1.pdbqt > file_1.pdb grep 'ATOM' file_1.pdb > file_1_lines_with_atoms_only.pdb Best wishes, Tomas On Thu, Apr 1, 2021 at 2:02 PM Fred Vellieux <[email protected]> wrote: > > Hello there, > > After running autodock vina on certain small molecules, the graphics > software I am using (e.g. Pymol, Coot) draws far too many bonds on the > docked small molecule. See enclosed screen capture. > > Is there any way to prevent this from happening? This isn't very > satisfactory of you wish to produce figures for a presentation or for > publication. > > Ta, > > Fred. > > -- > MedChem, 1st F. Medicine, Charles University > BIOCEV, Vestec, Czech Republic > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
