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
On Wed, Jul 23, 2014 at 12:48 PM, Harry Mark Greenblatt <
harry.greenbl...@weizmann.ac.il> wrote:
> BS"D
>
> Dear All,
>
> I thought I saw something about using get_area to get a residue by
> residue value for solvent accessible surface area, instead of the a per
> atom list. But I can't seem to find that now. Any ideas?
>
> In relation to this, when using the load_b option, can one redirect the
> output of "b" to a file within the command line (iterate object, print b)?
>
> Thanks
> Harry
>
>
>
> -------------------------------------------------------------------------
>
> 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
>
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Want fast and easy access to all the code in your enterprise? Index and
> search up to 200,000 lines of code with a free copy of Black Duck
> Code Sight - the same software that powers the world's largest code
> search on Ohloh, the Black Duck Open Hub! Try it now.
> http://p.sf.net/sfu/bds
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
