[phenixbb] cis peptide and pdb head
PAfonine at lbl.gov
Mon Aug 20 19:56:22 PDT 2007
> How does phenix.refine treat cis peptide? Will it automatically detect
> it and restrain it like refmac5? or do I have to input the information
Ralf is better person to answer since he implemented this... Anyway,
from what I remember, phenix.refine tries to automatically detect
cis/trans as following (Ralf, please confirm or deny):
- if in input model it deviates within 45 degrees from cis, then
phenix.refine considers it as cis;
- if in input model it deviates within 45 degrees from trans, then
phenix.refine considers it as trans.
> or generally how does phenix.refine treat the pdb head? I remember
> that some earlier version manual stated that all the head information
> are discarded, is that correct?
The only information that phenix.refine picks up and uses from PDB file
header is CRYST1 record. If data file in MTZ format is used then CRYST1
record is not mandatory.
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