Re: [COOT] Linking two sidechains with a double bond and refining
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 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=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=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/
Re: [COOT] 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=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/
[COOT] Linking two sidechains with a double bond and refining
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=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/
