Rms
Revision as of 05:48, 20 November 2013 by Hongbo zhu (talk | contribs) (the user comments section in page intra_rms referred by this page had been removed for irrelevance. Based on its importance the section is copied here.)
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Rms computes a RMS fit between two atom selections, but does not tranform the models after performing the fit.
USAGE
rms (selection), (target-selection)
EXAMPLES
fit ( mutant and name ca ), ( wildtype and name ca )
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.