Intra rms

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intra_rms calculates rms fit values for all states of an object over an atom selection relative to the indicated state. Coordinates are left unchanged. The rms values are returned as a python array.


cmd.intra_rms( string selection, int state)


from pymol import cmd
rms = cmd.intra_rms("(name ca)",1)


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, Rms_Cur, Intra_Fit, Intra_Rms_Cur, Pair_Fit