Re: [COOT] disulfide bond breaks in coot 0.9.6
On 11/05/2022 22:28, Kenneth Satyshur wrote: I have a disulfide bond defined in the pdb as SSBOND. It shows up in coot as a link between the sulfur atoms. But when I use 'sphere refine' the link is broken and there is no disulfide bond. That doesn't sound right. How close are the SG atoms? The same happens for my CYS to ZN ligands. That's completely different. They are defined with a 'LINK' line in the pdb. OK. So coot should use the metal restraints then. How do I tell 'sphere refine' to not break these links? Do I need to define a restraint explicitly? You shouldn't need to - it should do the right thing. But it seems like it isn't doing so in this case - that sounds like a bug. Paul. 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/
[COOT] disulfide bond breaks in coot 0.9.6
I have a disulfide bond defined in the pdb as SSBOND. It shows up in coot as a link between the sulfur atoms. But when I use 'sphere refine' the link is broken and there is no disulfide bond. The same happens for my CYS to ZN ligands. They are defined with a 'LINK' line in the pdb. How do I tell 'sphere refine' to not break these links? Do I need to define a restraint explicitly? thanks Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, College of Ag and Life Sciences: Department of Bacteriology; School of Medicine and Public Health: Departments of Biomolecular Chemistry, Neuroscience, Oncology, and Carbone Cancer Center (Small Molecule Screening Facility) University of Wisconsin-Madison Madison, Wisconsin, 53706 608-215-5207 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/
