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


===EXAMPLES===
===USER COMMENTS===
  fit ( mutant and name ca ), ( wildtype and name ca )
 
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===
[[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]]
[[Fit]], [[Rms_Cur]], [[Intra_Fit]], [[Intra_Rms]], [[Intra_Rms_Cur]], [[Pair_Fit]]


[[Category:Commands|rms]]
[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 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.

SEE ALSO

Fit, Rms_Cur, Intra_Fit, Intra_Rms, Intra_Rms_Cur, Pair_Fit

Warren DeLano's comment on rms_* and commands.

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