One possibility is this:
By default, REFMAC decided something is a cis-peptide if the omega
angle is < 90.0 .
It also reads and believes any CISPEP records you have in your input pdb.
(You can turn this feature off by requesting REFMAC to only restrain to
a cis peptide if you have a CISPEP record in your input pdb.)
Once the cis restraints are imposed the output PDB file will have
CISPEP records for all restrained residues. Many of these are unlikely,
and you may well correct them when rebuilding.
However the pdb file output by COOT will retain the CISPEP records.. You
need to check and edit these yourself..
Eleanor
anil kumar wrote:
Dear All,
I am refining a structure (resolution 2.4A) using Refmac and am getting a lot of cis-peptides (about 16 for prolines as well as other amino acids). There are some side chain swaps as well leading to high differences Rfactor: 20.6 and Rfree: 27.6. Although I tried to convert them to trans form and then tried to refine but it shows them again as cis peptides only.
In order to rectify the second problem of side chain swaps I have tried to mutate back the residues followed by refinements but it is also of no use.
I need to know if anyone of you have ever encountered these kind of problems. I will be greatly helped by your suggestions in this regard.
Best regards,
Anil Kumar (Graduate Student)
---------------------------------------------
School of Biological Sciences
Division of Structural & Computational Biology
Nanyang Technological University, 60 Nanyang Drive
Singapore 639798.
anil0...@ntu.edu.sg
Tel: +65-6316-2926
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