Editing Rms

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

===USAGE===
<source lang="python">
rms (selection), (target-selection)
</source>
===EXAMPLES===
<source lang="python">
fit ( mutant and name ca ), ( wildtype and name ca )
</source>

===USER COMMENTS===

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.

===SEE ALSO===
[[Fit]], [[Rms_Cur]], [[Intra_Fit]], [[Intra_Rms]], [[Intra_Rms_Cur]], [[Pair_Fit]]

[http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg00001.html Warren DeLano's comment on rms_* and commands.]
[[Category:Commands|Rms]]
[[Category:Structure_Alignment|Rms]]