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Hello--
>
> I have a cis proline in my strucutre. In anneal.py Iput cis peptide and it
> calculate the structure with cis. but when I take the best strucutre from
> that and put it in refine.py it gets trans. Can you suggest me what should
> I do to keep the peptide in cis form while using refine.py
>
Two options:
1) load a pre-generated PSF using protocol.initStruct, and then load
the structure with protocol.initCoords instead of protocol.loadPDB.
2) load the structure with protocol.loadPDB, and then correct the PSF
information using psfGen.cisPeptide.
It would be nice if loadPDB automatically identified cis-peptides, and
configured the PSF appropriately. Perhaps in the future...
best regards--
Charles
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