BS"D
Dear Andreas,
Thanks very much for the help....
Harry
On Jul 23, 2014, at 2:34 PM, Andreas Warnecke wrote:
Hej Harry,
This PyMOL wiki page may help you out further, it may be hard to find without
the underscore in the name:
http://www.pymolwiki.org/index.php/Get_Area
If you use the load_b=1 option, PyMOL will overwrite the b-factor.
You could select the atom by the overwritten b-factor, e.g.:
select mysele, b>5
Note this works for labeling, too.
label all, "%.2f"%b
You can use print to output the b-factor for each atom (the first part is just
to get the atom macro name):
cmd.iterate('all', 'print "/%s/%s/%s/%s`%s/%s`%s, %f" %(model, segi, chain,
resn, resi, name, alt, b)')
# note to replace 'all' by your selection name
Or if you prefer a file:
#####
python
from pymol import stored
stored.b_load=[]
cmd.iterate('all', 'stored.b_load.append("/%s/%s/%s/%s`%s/%s`%s, %f" %(model,
segi, chain, resn, resi, name, alt, b))')
f=open('report.txt','w')
for x in stored.b_load:
f.write(x+"\n")
f.close()
python end
#####
The report is comma separated and good for EXCEL import.
Hope this helps you out.
Cheers,
Andreas
-------------------------------------------------------------------------
Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology
Weizmann Institute of Science Phone: 972-8-934-3625
234 Herzl St. Facsimile: 972-8-934-4159
Rehovot, 76100
Israel
harry.greenbl...@weizmann.ac.il<mailto:harry.greenbl...@weizmann.ac.il>
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