Intra rms
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DESCRIPTION
"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.
PYMOL API
cmd.intra_rms( string selection, int state)
PYTHON EXAMPLE
from pymol import cmd
rms = cmd.intra_rms("(name ca)",1)
USER EXAMPLES/COMMENTS
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.
SEE ALSO
Fit, Rms, Rms_Cur, Intra_Fit, Intra_Rms_Cur, Pair_Fit