[phenixbb] Number of atoms and average b-factors for specific chain IDs (with the option of specifying multiple chain IDs).

det102 at uoxray.uoregon.edu det102 at uoxray.uoregon.edu
Sat Mar 13 11:26:44 PST 2010

    While I realize this is not a Phenix solution and this is a
Phenix bb I have to suggest:  You could just import your
coordinates into a spreadsheet and ask for the number of rows
and the average of the B factor column.

    On the other hand, I've never understood why the PDB requires
us to enter information that they could easily calculate from
the model for themselves...

Dale Tronrud

Ralf W. Grosse-Kunstleve wrote:
>> Is there anyway to get this quickly? Either by phenix util, web util,  
>> or whatever?
> Number of atoms is easy:
>   phenix.pdb_atom_selection your.pdb 'chain A or chain B'
> For the average B-factor you'll have to go to Python:
> import iotbx.pdb
> from cctbx.array_family import flex
> import sys
> pdb_inp = iotbx.pdb.input(file_name=sys.argv[1])
> hierarchy = pdb_inp.construct_hierarchy()
> sel = hierarchy.atom_selection_cache().selection("chain A or chain B")
> print "number of atoms:", sel.count(True)
> print "mean b:", flex.mean(hierarchy.select(sel).atoms().extract_b())
> Save to a file and run with "phenix.python".
> Ralf
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