[phenixbb] Number of atoms and average b-factors for specific chain IDs (with the option of specifying multiple chain IDs).
Francis E Reyes
Francis.Reyes at Colorado.EDU
Sat Mar 13 15:47:05 PST 2010
It's for NSMB, they actually ask for this stuff in their table 1 x-ray template.
Francis Reyes M.Sc.
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, det102 at uoxray.uoregon.edu 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)
>> 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".
>> phenixbb mailing list
>> phenixbb at phenix-online.org
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