Difference between revisions of "Average b"
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==usage== | ==usage== | ||
− | *copy code to text file and save as average_b.py. | + | * copy code to text file and save as average_b.py |
− | * | + | * type "run average_b.py" in PyMOL |
+ | * then type "average_b (selection)" | ||
==author== | ==author== | ||
Line 14: | Line 15: | ||
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> | ||
Latest revision as of 13:55, 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
- type "run average_b.py" in PyMOL
- 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)