[phenixbb] Multiple pdb entries in phenix.fmodel

Pavel Afonine pafonine at lbl.gov
Wed May 11 13:50:53 PDT 2011


yes, you can split your model into several PDB files and give it to 
phenix.refine: internally it will combine all input PDB contents into 
one model and use it.

You can also use
iotbx.pdb.join_fragment_files A.pdb B.pdb C.pdb
to merge multiple PDB file into one.

Note, multiple model files (files containing several models split by 
MODEL-ENDMDL) are not supported in phenix.refine, although supported in 
phenix.model_vs_data, phenix.maps, phenix.fmodel, etc.


On 5/11/11 1:43 PM, zhangh1 at umbc.edu wrote:
> Hi,
> I just wonder for the huge systems which have been split multiple pdb
> entries, if I provide all the pdb files in a single script of
> phenix.refine:
> phenix.fmodel A.pdb B.pdb C.pdb data.mtz
> whether everything will go correctly? Or I have to merge them into a
> single pdb and renumber all atoms sequentially?
> Thanks!
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