Hi Nidhi -

The “Align” feature in the GUI uses PyMOL's `align` command, which performs a sequence alignment to use as the basis for structural alignment.  It only uses those residues which match exactly, which can throw off the RMSD.  Try using `super` or `cealign` instead, which are structural alignments.  For example, assuming you have named selections for your active site residues:

super active_site_1, active_site_2

With `super`, the first selection is mobile, and is superimposed onto the second selection.  For `cealign`, switch the order of the arguments.

http://www.pymolwiki.org/index.php/Super
http://www.pymolwiki.org/index.php/Cealign

Cheers,
Jared

(Also, sorry for the duplicate message—I forgot to Reply All the first time.)
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Aug 9, 2014, at 6:12 AM, Nidhi Jatana <nidhijatana@bic-svc.ac.in> wrote:

Dear Sir/Madam

I have generated five models for a protein and I wanted to check the RMSD of only the binding site residues. I have the list of binding site residues. I tried using this through graphics by selecting the residues and then aligning by selection but somehow its giving me a higher RMSD than the entire structure but this should not happen. What is the other way to align specific residues?

Thanking you

Regards

--
Nidhi Jatana
Senior Research Fellow
Bioinformatics Center
Sri Venkateswara College
(University of Delhi)
Dhaula Kuan
New Delhi-110021.
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