Hi Fred, are you using the output from vina directly (I think it is called pdbrq)? If so, you could try converting it to mol2, before loading it into pymol.
Cheers, Johannes Am Do., 1. Apr. 2021 um 15:59 Uhr schrieb Robbie Joosten < [email protected]>: > 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 <[email protected]> On Behalf Of Fred > > Vellieux > > Sent: Thursday, April 1, 2021 15:02 > > To: [email protected] > > 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/ > ######################################################################## 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/
