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===DESCRIPTION===
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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.
 
  
 
===USAGE===
 
===USAGE===
rms (selection), (target-selection)
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<source lang="python">
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rms (selection), (target-selection)
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</source>
 +
===EXAMPLES===
 +
<source lang="python">
 +
fit ( mutant and name ca ), ( wildtype and name ca )
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</source>
  
===EXAMPLES===
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===USER COMMENTS===
  fit ( mutant and name ca ), ( wildtype and name ca )
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 +
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
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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
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won't work, due to the aforementioned reason.  To fix this, one needs to do,
 +
 +
alter all,segi=""
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alter all,chain=""
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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===
[[Cmd fit|fit]], [[Cmd rms_cur|rms_cur]], [[Cmd intra_fit|intra_fit]], [[Cmd intra_rms|intra_rms]], [[Cmd intra_rms_cur|intra_rms_cur]], [[Cmd pair_fit|pair_fit]]
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[[Fit]], [[Rms_Cur]], [[Intra_Fit]], [[Intra_Rms]], [[Intra_Rms_Cur]], [[Pair_Fit]]
  
[[Category:Commands|rms]]
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[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 03:09, 28 March 2014

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.

SEE ALSO

Fit, Rms_Cur, Intra_Fit, Intra_Rms, Intra_Rms_Cur, Pair_Fit

Warren DeLano's comment on rms_* and commands.