On 14/02/2023 09:28, Zeelen, Johan Philip wrote:
Dear All,
I am using Coot 0.9.8.7 EL (ccp4) on a macOS 10.15.7 and have the
following problems.
I am refining structures with 2 SS-bridges close together. When I use
Sphere Refine+ the refinement gives me a cluster of the 4 Cys.
molecules. See image.
Urgh. I thought that I'd fixed that by only allowing SSBOND linking.
Baah. Do you have a PDB code to hand so that I can reproduce this?
Second problem when I am using Change Chain ID to rename the
carbohydrates, the sugar molecules get changed, but not the
corresponding LINK entries.
OK. I'll add it to the list.
Third problem, several proteins are also O-linked glycosylated when I
try to upload the pdb to wwPDB Validation, after a local refinement in
Coot (but also after Phenix.refine or PDB-REDO) most of the GLC
molecules have a major validation issue PLANAR or WRONG HAND. Does
anyone have a solution?
That sounds like a fascinating link restraints problem. Coot will tell
you which link its trying to apply, I think. It is your job to check
that the link geometry is correct (or what you want).
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/
