Difference between revisions of "Average b"

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(code: adjusted string outputs to use string formatting instead of concatenation; adjusted whitespace around operators)
 
Line 14: Line 14:
 
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: ", selection
+
print "Your selection: %s" % selection
print "sum of B factors: ", stored.tempfactor
+
print "sum of B factors: %s" % stored.tempfactor
print "number of atoms: ",stored.atomnumber
+
print "number of atoms: %s" % stored.atomnumber
averagetempfactor=stored.tempfactor/stored.atomnumber
+
averagetempfactor = stored.tempfactor / stored.atomnumber
print "average B of '", selection,"': ", averagetempfactor
+
print "average B of '%s': %s" % (selection, averagetempfactor)
cmd.extend("average_b",average_b)
+
cmd.extend("average_b", average_b)
 
</source>
 
</source>
  

Latest 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)