Re: [PyMOL] find pairs?

[Jason V. <jas...@sc...>]

Bradley,

Short answer no.  Code like this could be included for
testing/development.  It gives me unexpected results sometimes, so if
you use it for any reason, be careful.

It finds all possible atom pairs between two selections under a given
distance cutoff and if you set 'mode' to 1 then within a given
angle-range compared to the optimal hydrogen bond vector.  This is not
finding hydrogen bonds.  Compare:

# grab a protein
fetch 1wld, async=0

# run find_pairs from all polymer atoms to
# the first organic small molecule
y = cmd.find_pairs("(poly)", "(bm. first organic)")
map(lambda aa: cmd.dist( "autoD", "index %s" % aa[0][1], "index %s" %
aa[1][1] ), y)

# show what we found
show dashes, autoD
show labels, autoD
color magenta, autoD
zoom autoD

...to the result of finding polar contacts between the first organic
small molecule ("bm. first organic") and the polymer ("polymer").
They're not equal.

Cheers,

-- Jason






On Fri, Aug 13, 2010 at 4:12 PM, Bradley Hintze
<bra...@ag...> wrote:
> I found this in the pymol user manule
>
>
> ################
>
> find_pairs
>
> DESCRIPTION
>
>   "find_pairs" is currently undocumented.
>
> ##################
>
> Is there anywhere that find_pairs has documentation or a good description??
>
> --
> Bradley J. Hintze
> Graduate Student
> Duke University
> School of Medicine
> 801-712-8799
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120