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Rms computes a RMS fit between two atom selections, but does not tranform the models after performing the fit.


rms (selection), (target-selection)


fit ( mutant and name ca ), ( wildtype and name ca )


To determine the RMS without any fitting, see Rms_Cur

Fit, Rms, Rms_Cur are finicky and only work when all atom identifiers match: segi, chain, resn, name, alt. If they don't then you'll need to use the alter command to change the identifiers to that they do -- typically that means clearing out the SEGI field, renaming chains, and sometimes renumbering.

I tried made two selections A, and D as

PyMOL>sel A, 1gh2 and n. CA and i. 65-99
Selector: selection "A" defined with 35 atoms.
PyMOL>sel D, 1kao and n. CA and i. 64-98
Selector: selection "D" defined with 35 atoms

which as you can see both yield 35 atoms. Now,

rms_cur A, D

won't work, due to the aforementioned reason. To fix this, one needs to do,

alter all,segi=""
alter all,chain=""
alter D, resi=str(int(resi)+1)  # I don't actually use this line

and now

rms_cur A, D

should work.


Fit, Rms_Cur, Intra_Fit, Intra_Rms, Intra_Rms_Cur, Pair_Fit

Warren DeLano's comment on rms_* and commands.