Re: [PyMOL] frustrating rms command

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

Hi,

On Tue, 16 Mar 2010 09:23:50 -0400 David Hall <li...@co...> wrote:

> See http://www.pymolwiki.org/index.php/Intra_Rms#USER_EXAMPLES.2FCOMMENTS
> comments that start with "Fit, Rms, Rms_Cur are finicky and only
> work..." as that likely explains your problem and a possible solution.
> 
> But I agree that pymol's behavior with this command can be extremely
> annoying.

I should have added to my previous e-mail that I wrote a script to take care
of this problem.  It will calculate the RMS for a pair of selections by
converting one to match the other (residue names, numbers, atom names etc. --
obviously only matching the backbone atoms).  It creates a new object in
order to do this.  The script is called fitting.py and can be found at my
pymol scripts site:

  http://pldserver1.biochem.queensu.ca/~rlc/work/pymol

and a description of the problems of fitting and an example of the use of
the fitting.py script can be found here:

   http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/

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