[phenixbb] links and REMARK 3 record in the final PDB

Pavel Afonine PAfonine at lbl.gov
Mon Feb 23 20:41:31 PST 2009

Hi Pascal,

phenix.refine does not write any LINK records to PDB file with refined 
model or any similar geometry restraints information.
All this information (all the information about geometry restraints used 
in refinement) is stored in .geo file.


On 2/23/09 11:33 AM, Pascal Egea wrote:
> Dear All,
> I apologize if this question has already been answered.
> I am refining a structure of a glycosylated-enzyme and I understood 
> the way to define all the links (N-glycosylation to the ASN and 
> beta-glycosidic bonds between the NAG units) and refinement is 
> complete and everything is good. All the links I included in my 
> cif_link definition file where taken into account and dealt with by 
> Phenix (the .def and .geo files are fine). Is it normal however that 
> in the resulting refined PDB file, no such links are written by PHENIX 
> under the REMARK 3 record ? Same thing for the 5 disulfide bonds 
> present in the protein.
> Thanks in advance for the clarification.
> Pascal Egea
> University of California San Francisco
> Department of Biochemistry and Biophysics 
> Laboratory of Robert Stroud 
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