Hi Fred, I think this is a problem of not having the right description of the compound. Have you tried using a restraint file for the compound in Coot so the bonds are properly defined? Note sure if Coot uses them, but perhaps also remove all the CONECT records.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Fred > Vellieux > Sent: Thursday, April 1, 2021 15:02 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] coot & other graphics programs draw too many bonds > > 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/
