Average b: Difference between revisions
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Jaredsampson (talk | contribs) (→code: adjusted string outputs to use string formatting instead of concatenation; adjusted whitespace around operators) |
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from pymol import cmd,stored | from pymol import cmd,stored | ||
def average_b(selection): | def average_b(selection): | ||
stored.tempfactor=0 | stored.tempfactor = 0 | ||
stored.atomnumber=0 | stored.atomnumber = 0 | ||
cmd.iterate(selection,"stored.tempfactor=stored.tempfactor+b") | cmd.iterate(selection, "stored.tempfactor = stored.tempfactor + b") | ||
cmd.iterate(selection,"stored.atomnumber=stored.atomnumber+1") | cmd.iterate(selection, "stored.atomnumber = stored.atomnumber + 1") | ||
print "Your selection: " | print "Your selection: %s" % selection | ||
print "sum of B factors: " | print "sum of B factors: %s" % stored.tempfactor | ||
print "number of atoms: " | print "number of atoms: %s" % stored.atomnumber | ||
averagetempfactor=stored.tempfactor/stored.atomnumber | averagetempfactor = stored.tempfactor / stored.atomnumber | ||
print "average B of ' | print "average B of '%s': %s" % (selection, averagetempfactor) | ||
cmd.extend("average_b",average_b) | cmd.extend("average_b", average_b) | ||
</source> | </source> | ||
Revision as of 12:32, 6 November 2013
average_b.py
- calculate the average B-factor of a selection.
usage
- copy code to text file and save as average_b.py. Install via Plugin>Install plugin from within PyMOL.
- restart PyMOL and then type "average_b (selection)"
author
Gregor Hagelueken
code
from pymol import cmd,stored
def average_b(selection):
stored.tempfactor = 0
stored.atomnumber = 0
cmd.iterate(selection, "stored.tempfactor = stored.tempfactor + b")
cmd.iterate(selection, "stored.atomnumber = stored.atomnumber + 1")
print "Your selection: %s" % selection
print "sum of B factors: %s" % stored.tempfactor
print "number of atoms: %s" % stored.atomnumber
averagetempfactor = stored.tempfactor / stored.atomnumber
print "average B of '%s': %s" % (selection, averagetempfactor)
cmd.extend("average_b", average_b)