Re: [PyMOL] directing output of "print"

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


Har...@we...<mailto:Har...@we...>