Difference between revisions of "Rms"
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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. | |
| − | |||
| − | |||
===USAGE=== | ===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=== | ===SEE ALSO=== | ||
| − | + | [[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:Commands|Rms]] | ||
| + | [[Category:Structure_Alignment|Rms]] | ||
Latest revision as of 05:48, 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.