RE: [PyMOL] anybody have experience with the "get_area" command?

[Warren D. <wa...@de...>]

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=3Dcmd.get_area("my_ligand")
target_area=3Dcmd.get_area("my_target")

# create the complex

create my_complex, my_ligand my_target

# measure the complex

complex_area=3Dcmd.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.                    =20
Principal Scientist

. DeLano Scientific LLC =20
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> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Thomas Stout
> Sent: Tuesday, April 18, 2006 10:36 AM
> To: pym...@li...
> Subject: [PyMOL] anybody have experience with the "get_area" command?
>=20
> =20
> Does it work?
> =20
> We're running version 0.99rc6 on both windoze and linux=20
> (RHEL,WS4) and the "get_area" command returns nothing (no=20
> error, no value).
> =20
> I've tried this with a number of situations, including=20
> loading a single object with a single protein chain and=20
> issuing "get_area all", "get_area n+c", "get_area /obj01" et=20
> cetera following the examples listed in Warren's former=20
> e-mail and subsequently replicated on the Wiki.
> =20
> "get_area ?" lists the syntax as "get_area [ selection [,=20
> state [, load_b [, quiet ]]]]", but "help get_area" does not help....
> =20
> Thanks for any suggestions,
> Tom
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