Re: [PyMOL] Pymol Align Command and RMSD Calculation ?

[Warren DeLano]

> 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 obj1CA, obj2CA
 
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

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[PyMOL] Regarding Object Find

[Suneel Kumar Bommisetty]

Dear All,



I am looking for script for "object find" In pymol. I have a sd file
contains 20 molecules. I have loaded into pymol. If I want visualize
next molecule, I need to press Play or forward or disply - sequence
function. Is there any script to/load/select/highlight specific molecule
from one object?



Please reply back



Thanks & Regards,

Suneel Kumar BVS










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