Hi, Not looking deep at your sequence/link, have you tried to move the link to a single bond and avoid the double as the linked bond? This way you can paraetrise the double bond correctly. Not sure is global phasing could help.. Joel
-----Original Message----- From: Mailing list for users of COOT Crystallographic Software <COOT@JISCMAIL.AC.UK> On Behalf Of David Dranow Sent: Tuesday, August 1, 2023 2:43 PM To: COOT@JISCMAIL.AC.UK Subject: Re: Linking two sidechains with a double bond and refining Message was attached instead of in the body for some reason. Here it is" Hi Learned Friends, I'm trying to refine a structure that has a very similar staple to the one in 8GJS. In that structure, there's a double bond between residue 5 and 12 in chain B. I've tried to define a link using jligand and I get a cif that looks like it would define the double bond. But when I load that into Coot and try to refine the link, the bond blows up, bonded atoms seperate. Has anyone had any luck with this? What should I use to define a double bond link such that Coot (and Phenix) doesn't blow it up, but also keeps the appropriate atoms in plane (either trans or cis, NOT something in between). Thanks, David ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of http://www.jiscmail.ac.uk/COOT, a mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
