Difference between revisions of "Rms"

From PyMOLWiki
Jump to: navigation, search
(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.)
 
Line 14: Line 14:
 
To determine the RMS without any fitting, see [[Rms_Cur]]
 
To determine the RMS without any fitting, see [[Rms_Cur]]
  
See [[Intra_Rms]] for selection caveats for this group of commands.
+
[[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]]
  
 +
[http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg00001.html Warren DeLano's comment on rms_* and commands.]
 
[[Category:Commands|Rms]]
 
[[Category:Commands|Rms]]
 
[[Category:Structure_Alignment|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.