Hello,
What about refining using refmac5 ?
it may yield to different results
Mahmoud Rizk
On 03/03/2022 15:15, Akanksha Tomar wrote:
Hi everyone,
I am trying to refine the occupancy of a bound ligand. After fixing
the protein model and water I fitted the ligand into it. Currently, I
am using Phenix Refine with occupancy refinement for individual atoms
switched on. After the refinement, the overall occupancy of the ligand
is 0.7 and the RSCC value is 0.86. The resolution of the structure is
2.1 Å.
Now the problem is that the program has assigned different occupancies
to different atoms of the ligand. For some cases, it has assigned 0
occupancies to atoms for which there is a clear positive peak.
Why it has been done so and is it acceptable?
Any help would be greatly appreciated.
Thank you.
--
Best Regards,
Akanksha Tomar
Pre-Doctoral Fellow,
C\o Dr. Arockiasamy Arulandu,
Membrane Protein Biology Group,
International Center for Genetic Engineering and Biotechnology,
New Delhi, India
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