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-archive.com/ccp4bb@jiscmail.ac.uk/msg51707.html
-James Holton
MAD Scientist
On 5/6/2024 12:19 PM, Liliana Margent wrote:
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 conformations for the cysteines.
Yet, when I endeavor to model alternate conformations for both cysteines, their
occupancies do not align despite running refinement with a bond parameter file
that specifies the link. To illustrate, I initiate the refinement with
occupancies for Cys472 as A0.75/B0.25 and for C384 as A0.75/B0.25, but
post-refinement, the output occupancies appear as Cys472 A0.84/B0.16 and for
C384 A0.97/B0.03. Where A confs participate in the s-s bond.
Has anyone else encountered this issue before, or does anyone have suggestions
on how to refine these cysteines to achieve coherent occupancies?
Thank you for any insights you can provide.
Best,
Liliana
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