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

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Sat Mar 13 11:09:25 PST 2010

> 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".


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