[phenixbb] explicit pdb output file name (refine)
PAfonine at lbl.gov
Wed Jan 20 22:21:14 PST 2010
in fact, phenix.refine outputs information about refined f' and f'' in
ready-to-PDB-deposit format under RAMARK 3 prefix. For eample:
REMARK 3 ANOMALOUS SCATTERER GROUPS DETAILS.
REMARK 3 NUMBER OF ANOMALOUS SCATTERER GROUPS : 2
REMARK 3 ANOMALOUS SCATTERER GROUP : 1
REMARK 3 SELECTION: name BR
REMARK 3 fp : -0.8792
REMARK 3 fdp : 5.8029
REMARK 3 ANOMALOUS SCATTERER GROUP : 2
REMARK 3 SELECTION: name CO
REMARK 3 fp : 0.0000
REMARK 3 fdp : 0.0000
I hope this information is preserved when such structures get deposited
into PDB -:)
On 1/20/10 9:44 PM, Ralf W. Grosse-Kunstleve wrote:
>> Do I understand correctly that there is no way to force refine to skip
>> the serial in the output pdb file name, i.e. foo.pdb, not foo_001.pdb?
> Yes, that's true.
> The main reason is that the same run writes
> When I implemented this I thought the serial numbers are the only
> practical way to keep things straight.
> Later we added storage of refined f' and f" to the .def file (since
> there is no place in the .pdb file that would survive passes through
> external programs). Because of this the serial numbers seem even more
> important to me.
> phenixbb mailing list
> phenixbb at phenix-online.org
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