[phenixbb] cis peptide and pdb head

[Jianghai Zhu]

After phenix.refine detects the cis peptide, where does this  
information output?

Jianghai

+++++++++++++++++++++++++++++++
Jianghai Zhu, Ph.D
CBR Institute for Biomedical Research
Department of Pathology
Harvard Medical School
200 Longwood Ave., Boston, MA 02115
Ph: 617-278-3211
Fx: 618-278-3232
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On Aug 20, 2007, at 10:56 PM, Pavel Afonine wrote:

> Hi Jianghai,
>
>> 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
>> somewhere?
>
> 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.
>
> Pavel.
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