Thank you so much
From: Eleanor Dodson
Date: Monday, May 6, 2024 at 3:30 PM
To: Liliana Margent
Cc: CCP4BB@jiscmail.ac.uk
Subject: [EXTERNAL]Re: [ccp4bb] Modeling Disulfide Bond Occupancies
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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.
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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
<176a9d
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?
https://www.mail
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 g
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, y
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
tha
