Relying on refinement to fix cis peptide bonds for you is unlikely to
end well. It looks to me like you really need to spend some time
investigating and manually rebuilding these first.
On 2017-10-10 13:52, 师扬 wrote:
Dear all,
I am refining a model based on a 4.3A EM density map,and there are
some cis-peptides in the beginning model.
By using phenix.real_space_refine with a very low cis-peptide
threshold (0), all the cis-peptide become to the twisted.
The start Omega angle:
cis-proline: 31.63 %
twisted proline: 0.00 %
cis-general: 11.11 %
twisted-general: 0.05 %
The final Omega angle:
cis-proline: 0.00 %
twisted proline: 27.55 %
cis-general: 0.00 %
twisted-general: 6.04 %
My questions are:
1) What is the twisted peptide?
2) Is the amount acceptable at the current resolution?
2) How to refine it?
Thanks in advance!
Yang Shi
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