Re: [PyMOL] directing output of "print"

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 <
har...@we...> 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
>
>
>  Har...@we...
>
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> 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 (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>