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".
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