Warren DeLano
Sun, 25 Oct 2009 07:03:24 -0700
> 1. What type of RMSD is calculated with align comman i.e All Atoms or only Backbone? It depends on the input selections. If you don't restrict it to backbone atoms, PyMOL will perform the fit for all matched atoms. Also, it is important to understand that "align" is a combined sequence and 3D refined structure alignment which, by default, iteratively discards outliers in order to achieve a well-matched core structure. "super" is similar except that it doesn't use sequence. > 2. If I have few models/PDB stuructures of the same protein how I can clauclate the total atoms and backbone only RMSD between these. Actually I am confused with usuage of these commands i.e align , super, rms, rms_cur etc. If you're trying to calculate RMS between specific pairs of atoms : If the proteins have matched identifiers (identical segment, chain, and residue identifier), then the command you want is "fit": # all atom fit obj1, obj2 # C-calpha only fit obj1////CA, obj2////CA If the protein do not have matched identifiers, then you must manually select exactly N atom pairs in each structure, and then use pair_fit: # C-alpha fit for residues 10 through 80 and 100 through 120 pair_fit obj1///10-80+100-120/CA, obj2///10-80+100-120/CA Cheers, Warren
________________________________ From: Bio Brain [mailto:biobr...@gmail.com] Sent: Sat 10/24/2009 1:11 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Pymol Align Command and RMSD Calculation ? Dear Pymol Users, I am looking for some very basic information about the PyMol commands. 1. What type of RMSD is calculated with align comman i.e All Atoms or only Backbone? 2. If I have few models/PDB stuructures of the same protein how I can clauclate the total atoms and backbone only RMSD between these. Actually I am confused with usuage of these commands i.e align , super, rms, rms_cur etc. Regards ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ 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
------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference
_______________________________________________ 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