Do not know what the resolution is here, try an anisotropic refinement of the
Cys side chains first to see if this solves your problem.
__
Dr. math. et dis. nat. Jeroen R. Mesters
University of Lübeck
https://orcid.org/-0001-8532-6699
Am 06.05.2024 um 21:48 schrieb Eleanor Dodson
In the CCP4 program refmac5, you specify occupancy groups and then
specify how to refine them. The setup, afaik, is not automatic.
Documentation for how to do it is here:
http://www.ysbl.york.ac.uk/refmac/data/refmac_keywords.html#Occupancy
You may also find this link helpful?
But are there two conformations of the disulphide? or one disulphide and
one broken link?
Eleaor
On Mon, 6 May 2024 at 20:42, Dr. Kevin M Jude wrote:
> I have done this in shelxl or phenix refinement, you can define occupancy
> groups (or free variables in shelxl) so that 472A and 384A are one
I have done this in shelxl or phenix refinement, you can define occupancy
groups (or free variables in shelxl) so that 472A and 384A are one group, 472B
and 384B are another. Pretty sure there is a similar solution in refmac. Though
also if the 384A rotamer doesn’t clash with the 472B rotamer,
Well - I turn off occupancy refinement once there is a sort of consensus..
Disulphides often break after long exposures and you see the positive and
negative blobs clearly. I must admit I usually just set 0.5 as occ , fix
the surviving disulphide link and let the B values suggest a better ratio
Greetings everyone,
I'm currently in the process of modeling a disulfide bond in two structures.
However, when I attempt to model single occupancy for the cysteines involved in
the bond, negative density blobs emerge within the disulfide bond. This
suggests the possibility of alternate
Dear all,
I have a 4-year PhD position in structural biology available in my research
group at Lund University. More details can be found at the link below. Please
spread the announcement to any suitable candidates you know. Last application
date is 20th May!
/Derek
Greetings!
I am learning the concept of multiple ligand simultaneous docking and would
like to know if there is any standard protocol for the same.
Thanking you in advance,
With regards,
Thripthi Shenoy.
To unsubscribe
