Hi David, Rob Nicholls gave a talk about AceDrg and link generation at a CCP4 SW a few years ago..
https://www.youtube.com/watch?v=p4oTJ0bjD3M I think this will contain the answers you are looking for. Cheers, David -- Dr David C. Briggs CSci MRSB (he/him) Principal Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK Working hours: Mon-Fri 0900-1700 == about.me/david_briggs<https://about.me/david_briggs> | OrcID<https://orcid.org/0000-0002-9793-7339> | Google Scholar <https://scholar.google.co.uk/citations?user=DRKG5KwAAAAJ> ________________________________ From: Mailing list for users of COOT Crystallographic Software <[email protected]> on behalf of David Dranow <[email protected]> Sent: 01 August 2023 03:43 To: [email protected] <[email protected]> Subject: Re: Linking two sidechains with a double bond and refining External Sender: Use caution. 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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=05%7C01%7C%7Ce82f2702ddfa489f37c308db923aa70b%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638264552849819547%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=lU3%2F1yIabSpWhJXqDIlhP4tN3r8SdES1OVY3MLWlVtI%3D&reserved=0<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1> This message was issued to members of https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCOOT&data=05%7C01%7C%7Ce82f2702ddfa489f37c308db923aa70b%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638264552849819547%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=EfY%2FZJw6%2FoaKFnvZiXVSHFnf%2BTbhBf382RPt%2B0UGW%2Fw%3D&reserved=0<http://www.jiscmail.ac.uk/COOT>, a mailing list hosted by https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C01%7C%7Ce82f2702ddfa489f37c308db923aa70b%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638264552849819547%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=t0ITOV3r5%2FimgrQSp376Atm4cxjIFMnzuytr%2B%2Ff1Efs%3D&reserved=0<http://www.jiscmail.ac.uk/>, terms & conditions are available at https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C01%7C%7Ce82f2702ddfa489f37c308db923aa70b%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638264552849819547%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=z8tJo%2B%2B9xL%2FcMnE10LLoEjUNlVNIkmIH7UM25dgAsyY%3D&reserved=0<https://www.jiscmail.ac.uk/policyandsecurity/> The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT ######################################################################## 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/
