[COOT] Linking two sidechains with a double bond and refining

2023-07-31 Thread David Dranow
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.

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

2023-07-31 Thread Joel Tyndall
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

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

2023-07-31 Thread David Dranow
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