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 <nidhijat...@bic-svc.ac.in<mailto:nidhijat...@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 [https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif]-- 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<mailto: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
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