[phenixbb] cis peptide and pdb head
jzhu at cbr.med.harvard.edu
Mon Aug 20 20:16:44 PDT 2007
After phenix.refine detects the cis peptide, where does this
Jianghai Zhu, Ph.D
CBR Institute for Biomedical Research
Department of Pathology
Harvard Medical School
200 Longwood Ave., Boston, MA 02115
On Aug 20, 2007, at 10:56 PM, Pavel Afonine wrote:
> Hi Jianghai,
>> How does phenix.refine treat cis peptide? Will it automatically
>> it and restrain it like refmac5? or do I have to input the
> 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
> header is CRYST1 record. If data file in MTZ format is used then
> record is not mandatory.
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> phenixbb at phenix-online.org
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