Re: [PyMOL] Show hydrogen bonds in current object only

[Robert C. <rob...@qu...>]

Hi Jason,

On Sun, 29 Nov 2009 12:29:08 -0500, Jason Vertrees <jas...@gm...>
wrote:

> You can automate the task.  Load your 100 proteins.  Use a wildcard
> from the command line or a script like loadDir
> (http://pymolwiki.org/index.php/LoadDir).  Align them.  Then, run:
> 
> python
> for n in cmd.get_names("objects"):
>   selName = "s" + n
>   cmd.select(selName, n)
>   cmd.distance("dist"+n, selName, selName + " and (organic and " + n + ")", 3.2, mode=2)
> python end

I'm just curious, but why do you go to the trouble to create a selection that
is just the whole object? Especially if Chimed has 100s of objects, he
doesn't need to add a named selection for each. Why not do the following?

python
for n in cmd.get_names("objects"):
  cmd.distance("dist"+n,n,n + " and organic",3.2, mode=2)
python end

The latter worked for me.  If you wanted to eliminate waters from
the selection for the protein, you could change it to:

python
for n in cmd.get_names("objects"):
  cmd.distance("dist"+n,n + " and not solvent",n + " and organic",3.2,mode=2) 
python end

Or to make it more readable:

python
for n in cmd.get_names("objects"):
  protein_sele = n + " and not solvent"
  organic_sele = n + " and organic"
  cmd.distance("dist"+n, protein_sele, organic_sele, 3.2, mode=2)
python end

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc