> 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:biobrain@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

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