Re: [PyMOL] alignment by residue

[Thomas H. <sp...@us...>]

Hi Sasi,

for "pair_fit" you have to match all atom pairs manually. I guess what 
you want is "align" on the full monomers and then "rms_cur" (or just 
distance measure) on each CA pair.

Have a look at the "rmsd_b.py" script from
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

It writes per residue deviation to the b-factor column.

Example:

fetch 2hv1, async=0
extract mono2, chain B
align mono2, 2hv1, cycles=0, object=aln
rmsd_b mono2 & aln, 2hv1 & aln
iterate mono2 and name CA, print (resi,b)

Hope that helps.

Cheers,
   Thomas

sasi kodathala wrote, On 12/27/11 01:37:
> dear pymol users,
> 
> i have a homodimer, with two identical monomers. i would like to know 
> the rmsd of each residue in the first monomer with respect to each 
> residue in the second monomer.
> 
> i guess pair_fit should give the rmsd.
> 
> is there a better command to look at the per residue rmsd.
> 
> thank you.
> 
> sasi

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen