IT could be miscommunication between refmac and coot. Try to remove
cispep lines from your pdb and refine again. Then it may work. After
model building info about cispep and/or ssbridge should be removed
from the pdb file (unless you are confident about them)
regards
Garib
On 25 Jan 2009, at 19:32, 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.
[email protected]
Tel: +65-6316-2926
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