[PyMOL] combine align and rms_cur to calculate rms for complexes

[Andrea S. <and...@gm...>]

Hi all,
could someone confirm this:
I have some complexes protein+ligand and I'd like to perform rms
calculation for the position of the ligand. This what I have done:

load reference.pdb
select proteinreference, segi A
select ligreference, segi B
load compare.pdb
select proteincomapre, segi A
select ligcompare, segi B
align proteinreference,proteincompare
rms_cur ligreference,ligcompare

is rms_cur the right command to calculate the rms for the ligand
position? then, is the procedure "chemically" correct?

thanks

regards,

andrea

--
"La conoscenza libera il genere umano dalla superstizione"
J. Watson