This is a read-only mirror of pymolwiki.org

Difference between revisions of "Rms"

From PyMOL Wiki
Jump to navigation Jump to search
m
 
m (10 revisions)
 
(3 intermediate revisions by 2 users not shown)
Line 1: Line 1:
===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.
  
Line 12: Line 11:
  
 
===USER COMMENTS===
 
===USER COMMENTS===
See [[Intra_Rms]] for selection caveats for this group of commands.
+
 
 +
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]]
  
 +
[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 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.