Tom,

Apologies for the confusion, but there really isn't any way to measure overall structural similarity in PyMOL other than pair_fit, but you have to do the work of explicitly stating which pairs are to be aligned.  

The pair_fit selections don't have to be identical, but they do have to correspond in a pairwise fashion.  In other words, you can compare any number of C-alpha positions so long as the same number of atomic positions are specified in each structure.

Cheers,
Warren

-----Original Message-----
From: Thomas Evangelidis [mailto:te8624@mbg.duth.gr]
Sent: Thu 10/29/2009 5:24 AM
To: Warren DeLano
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] how to get RMSD from align command

Hi Warren,

Now I am more confused. I used align command to measure the overall 
RMSD between homologous structures. Apparently align is not 
appropriate if not sufficient sequence similarity is present. I later 
came across CEalign plugin, which does structure-based 
superimposition. This command also returns an RMSD value, which 
happens to be higher for the set of homologous structures I analysed. 
Based on this I concluded that align command is more appropriate to 
measure measure structural similarity, but I'm not sure now.

My objective is to select between a small set of homologous structures 
(co-crystallized with ligands), the one with the highest structural 
similarity and use it to place a dummy ligand into one where it's 
missing. I.e. "1ebh" lacks a ligand, so I compared it with "1ebg", 
"1els", "1one", "2one", "5enl", "6enl", "7enl" which have 
co-crystallized ligands. According to both align and cealign, 5ENL is 
the most similar with overall RMSD 0.246 and 0.420907 respectively. 
The question is which command produces the best superimposition 
provided that these proteins belong to the enolase family and thus 
have high sequence and structural similarity? Based on the RMSD 
values, align does, but as you said this value pertains to only a 
subset of atoms after refinement.

Apparently pair_fit command cannot be used for my purpose as it 
requires identical selections.

Tom


> Tom,
>
> The complication with cmd.align() is that it is doing a whole lot 
> more than a simple alignment.  The first number is in fact the RMS, 
> but it covers only the subset of the input atoms remaining after 
> refinement is completed. The count of aligned atoms is the second 
> field.
>
> If you're looking for exact RMS fit values over a well-defined set 
> of atoms, try using cmd.pair_fit(sele1, sele2) instead, for example:
>
> load $TUT/1hpv.pdb
>
> create loopA, A/46-55/
>
> create loopB, B/46-55/
>
> show sticks, loop*
>
> print cmd.pair_fit("loopA////CA", "loopB////CA")
>
> Cheers,
> Warren
>
> -----Original Message-----
> From: Thomas Evangelidis [mailto:te8624@mbg.duth.gr]
> Sent: Wed 10/28/2009 8:09 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] how to get RMSD from align command
>
> Simple question, it must have been answered before but couldn't find
> it so far:
>
> how can I get the RMSD value from the align command in a python
> script? cmd.align() returnes a tuple of 8 numbers and none of them is
> the actual RMSD value I get when I align these 2 structures manually.
>
> thanks,Tom
>
>
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----- End message from warren@delsci.com -----



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