Difference between revisions of "Average b"
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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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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: %s" % selection | + | print("Your selection: %s" % selection) |
| − | print "sum of B factors: %s" % stored.tempfactor | + | print("sum of B factors: %s" % stored.tempfactor) |
| − | print "number of atoms: %s" % stored.atomnumber | + | print("number of atoms: %s" % stored.atomnumber) |
averagetempfactor = stored.tempfactor / stored.atomnumber | averagetempfactor = stored.tempfactor / stored.atomnumber | ||
| − | print "average B of '%s': %s" % (selection, averagetempfactor) | + | 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 13:38, 26 April 2023
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)