This is a read-only mirror of pymolwiki.org

Difference between revisions of "Average b"

From PyMOL Wiki
Jump to navigation Jump to search
(New page: =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 P...)
 
Line 3: Line 3:
 
*calculate the average B-factor of a selection.
 
*calculate the average B-factor of a selection.
  
==Usage==
+
==usage==
 
*copy code to text file and save as average_b.py. Install via Plugin>Install plugin from within PyMOL.
 
*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)"
 
*restart PyMOL and then type "average_b (selection)"
  
==Contact==
+
==author==
Gregor Hagelueken,
+
Gregor Hagelueken
gh50@st-andrews.ac.uk
 
  
==Code==
+
==code==
 
<source lang="python">
 
<source lang="python">
 
from pymol import cmd,stored
 
from pymol import cmd,stored
Line 20: Line 19:
 
cmd.iterate(selection,"stored.atomnumber=stored.atomnumber+1")
 
cmd.iterate(selection,"stored.atomnumber=stored.atomnumber+1")
 
print "Your selection: ", selection
 
print "Your selection: ", selection
print "sum of b factors: ", stored.tempfactor
+
print "sum of B factors: ", stored.tempfactor
 
print "number of atoms: ",stored.atomnumber
 
print "number of atoms: ",stored.atomnumber
 
averagetempfactor=stored.tempfactor/stored.atomnumber
 
averagetempfactor=stored.tempfactor/stored.atomnumber
print "average b of '", selection,"': ", averagetempfactor
+
print "average B of '", selection,"': ", averagetempfactor
 
cmd.extend("average_b",average_b)
 
cmd.extend("average_b",average_b)

Revision as of 08:08, 17 December 2008

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

<source lang="python"> 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: ", selection print "sum of B factors: ", stored.tempfactor print "number of atoms: ",stored.atomnumber averagetempfactor=stored.tempfactor/stored.atomnumber print "average B of '", selection,"': ", averagetempfactor cmd.extend("average_b",average_b)