Re: [PyMOL] Script for iterated `align`ment & API for CEalign

[Jason V. <jav...@ut...>]

DimitryASuplatov,

> I have 21 pdb files in my folder. I wrote a small script to load them
> all at once to the Pymol

[...snip...]

> I have found a pymol wiki article about CEalign
> (http://www.pymolwiki.org/index.php/Cealign) - structure alignment
> procedure that is claimed to be better than align and super since it
> primarily aligns structures, not sequences.
> I did not find any API for CEalign. Does anybody now how could I launch
> cealign from a script?

I wrote the CEAlign plugin for PyMOL.  First, you can easily align all
your structures to one using the "alignto" extension of CEAlign.  This
will automatically align all other objects to whatever one you specify.
 It's just a simple wrapper for CEAlign.

To use it in a script (requires CEAlign and that CEAlign be loaded), try
the following:
"""
#
# example PyMOL script, save as 'ex.pml' run with pymol -cq ex.pml
#
from pymol import cmd
cmd.fetch("1cll")
cmd.fetch("1ggz")
cmd.fetch("1sra")
alignto("1cll")
"""

Output:
Aligning 1cll to 1cll
RMSD 0.000000 over 144 residues
Aligning 1ggz to 1cll
RMSD 4.254369 over 136 residues
Aligning 1sra to 1cll
RMSD 3.086769 over 64 residues

You can parse the output, or change the alignto command to suit your needs.

Lastly, there are a couple things to keep in mind, due to algorithmic
complexities & the nature of proteins:

  (1) If you're doing "hard" structure alignments -- similar structures
with low sequence identity, then I would suggest using CEAlign.

  (2) If you're doing easy alignments -- those with high sequence
identity, use 'super'.

  (3) If you're trying to align the same structure to itself (say
different states of an NMR or MD ensemble) then use optAlign, which
comes with CEAlign & Kabsch.  It's provably optimal, hence the name.

Refs:
CEAlign -- http://www.pymolwiki.org/index.php/Cealign
Super   -- http://www.pymolwiki.org/index.php/Super
optAlign-- http://www.pymolwiki.org/index.php/Kabsch

HTH,

-- Jason

-- 

Jason Vertrees, PhD

Dartmouth College : jv...@cs...
Boston University : ja...@bu...

PyMOLWiki : http://www.pymolwiki.org/