Re: [PyMOL] align

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

Hi David,

On Mon, Nov 29, 2010 at 10:33 AM, David A.  Horita <dh...@wf...> wrote:
> Hi - a couple align questions:
> 1.  How do I get a listing of which atoms are used for alignment/RMSD
> calculation when aligning one molecule to another via the align to molecule
> pulldown (especially if they're different proteins)

You can iterate over the the new alignment objects.  Here's an example,

# fetch some proteins
fetch 1rlw 1rsy, async=0

# align them, save to an alignment 'object'
align 1rlw, 1rsy, object=aln

# walk over the alignment object for each protein
# and print out the included alpha carbons
iterate aln and 1rlw and n. CA, print model, chain, resi, resn, name, elem
iterate aln and 1rsy and n. CA, print model, chain, resi, resn, name, elem

You can iterate across other properties as you see fit.


> 2.  Is it possible to write an alignment script, e.g., align mol2 and (name
> n,c,ca) and (resid 10-64), mol1 and ...
> where mol2 and mol1 are generic labels for the first, second, etc. molecules
> loaded?  I'm looking at NMR structure bundles where each conformer has a
> name from e.g., refined_1 to refined_16, and aligning each of them pairwise
> to the first in the set.  If I only load in a subset - say the 4 lowest
> energy, they may or may not include any given filename, so aligning them to
> an explicit name won't always work.

There's no default "molX" or equivalent.  I suggest you use the
"get_names" function.  In the following example, it'll return a list
of names of objects and align that to your target protein called
'target':

for conformerX in cmd.get_names("objects"):
  cmd.align(conformerX, "target")

As a more concrete example, the target is "3kus":

# fetch a multistate protein
fetch 1nmr 3kus, async=0, multiplex=1

python
for x in cmd.get_names("objects"):
  if "1nmr" in x:
    cmd.align(x, "/3kus//B")
python end

For any keywords here like "discrete," "multiplex," "cmd", be sure to
check the PyMOLWiki (http://pymolwiki.org) for more information.

Cheers,

-- Jason

> Thanks,
> David
>
> -----------------------------
> David A. Horita, Ph.D.
> Department of Biochemistry
> Wake Forest University School of Medicine
> Winston-Salem, NC 27157-1016
> Tel: 336 713-4194
> Fax: 336 716-7671
> email:  dh...@wf...
> web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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