Re: [PyMOL] distances

[Thomas H. <sp...@us...>]

Hi Krisztina,

the syntax for the "around" operator is wrong, there is no "of" keyword.

One of these would be correct:
hcpl1 within 5 of hcpl2
hcpl2 around 5 and hcpl1

See also:
http://pymolwiki.org/index.php/Selection_Algebra#Comparison_of_distance_operators

To iterate over atoms of a selection, you can use "cmd.pop". There is no 
PyMOLWiki page, but you'll get a nice example from:
PyMOL> help pop

Also very powerful for iteration over atoms:
http://pymolwiki.org/index.php/Iterate

What you actually want is to iterate over distances, not atoms. There is 
a script on the PyMOLWiki which provides that:
http://pymolwiki.org/index.php/Get_raw_distances

cmd.distance('tmp', 'hcpl1' ,'hcpl2', 5.0)
for (i1, i2, dst) in get_raw_distances('tmp'):
   f.write("%8.3f\n" % dst)

Hope that helps.

Cheers,
   Thomas

On 30.07.2012 19:34, Krisztina Feher wrote:
> Hi Everyone,
>
> I would like to write a script, which writes out intermolecular
> distances shorter than 5A between hydrogens into a text file. Here is
> what I made so far on the basis of the Measure distance script in the
> respository:
>
> from pymol import cmd
>
> # open dist.txt for writing
> f=open('dist.txt','w')
>
> hcpl1=cmd.select('hcpl1', 'resi 1-10 and hydro')
> hcpl2=cmd.select('hcpl2', 'resi 11-20 and hydro')
> inoe12=cmd.select('inoe12', 'hcpl1 around 5 of hcpl2')
>
> for i in range(len(hcpl1)):
> dst=cmd.distance('tmp', 'hcpl1' ,'hcpl2')
> f.write("%8.3f\n"%dst)
> f.close()
>
> What do not understand is the following:
> - why inoe12 selection is not being made (it works from pymol command
> line as
> "select inoe12, hcpl1 around 5 of hcpl2" )
> - how can I loop over the atoms of a selection (hcpl1 seems to be not a
> list, but a single interger)
>
> Thanks for any help in advance!
> Krisztina

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen