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.



(Also, sorry for the duplicate message—I forgot to Reply All the first time.)
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center

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


Nidhi Jatana
Senior Research Fellow
Bioinformatics Center
Sri Venkateswara College
(University of Delhi)
Dhaula Kuan
New Delhi-110021.
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net