It's for NSMB, they actually ask for this stuff in their table 1 x-ray template. FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D On Mar 13, 2010, at 12:26 PM, [email protected] wrote:
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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