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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. | [[Rms]] computes a RMS fit between two atom selections, but does not tranform the models after performing the fit. | ||
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===USER COMMENTS=== | ===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=== | ===SEE ALSO=== | ||
[[Fit]], [[Rms_Cur]], [[Intra_Fit]], [[Intra_Rms]], [[Intra_Rms_Cur]], [[Pair_Fit]] | [[Fit]], [[Rms_Cur]], [[Intra_Fit]], [[Intra_Rms]], [[Intra_Rms_Cur]], [[Pair_Fit]] | ||
[[Category:Commands| | [http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg00001.html Warren DeLano's comment on rms_* and commands.] | ||
[[Category:Structure_Alignment]] | [[Category:Commands|Rms]] | ||
[[Category:Structure_Alignment|Rms]] | |||
Latest revision as of 04:48, 20 November 2013
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.