Hi Tom,
There are some pitfalls with get_area that have led me to recommend against its
use until we can prepare some more comprehensive documentation and examples for
its use. If you have other tools for measuring areas, then I recommend using
them instead. If not, then here is a partial example:
# load components separately
load my_ligand.pdb
load my_target.pdb
# get hydrogens onto everything (NOTE: must have valid valences on the
ligand...)
h_add
# make sure all atoms within an object occlude one another
flag ignore, none
# use solvent-accessible surface with high sampling density
set dot_solvent, 1
set dot_density, 3
# measure the components individually
ligand_area=cmd.get_area("my_ligand")
target_area=cmd.get_area("my_target")
# create the complex
create my_complex, my_ligand my_target
# measure the complex
complex_area=cmd.get_area("my_complex")
# now print results
print ligand_area
print target_area
print complex_area
print (ligand_area + target_area) - complex_area
Cheers,
Warren
BTW: thanks for your suggestions about quit/close warnings!
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:war...@delsci.com
> -----Original Message-----
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Thomas Stout
> Sent: Tuesday, April 18, 2006 10:36 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] anybody have experience with the "get_area" command?
>
>
> Does it work?
>
> We're running version 0.99rc6 on both windoze and linux
> (RHEL,WS4) and the "get_area" command returns nothing (no
> error, no value).
>
> I've tried this with a number of situations, including
> loading a single object with a single protein chain and
> issuing "get_area all", "get_area n+c", "get_area /obj01" et
> cetera following the examples listed in Warren's former
> e-mail and subsequently replicated on the Wiki.
>
> "get_area ?" lists the syntax as "get_area [ selection [,
> state [, load_b [, quiet ]]]]", but "help get_area" does not help....
>
> Thanks for any suggestions,
> Tom
>
>
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