Difference between revisions of "Intra rms"

From PyMOLWiki
Jump to navigation Jump to search
m
(user comments had been removed for its irrelevance. They are copied to rms page given its importance and add a link to the page.)
 
(3 intermediate revisions by 3 users not shown)
Line 1: Line 1:
−
===DESCRIPTION===
 
 
'''intra_rms''' calculates rms fit values for all states of an object over an atom selection relative to the indicated state.  Coordinates are left unchanged.  The rms values are returned as a python array.
 
'''intra_rms''' calculates rms fit values for all states of an object over an atom selection relative to the indicated state.  Coordinates are left unchanged.  The rms values are returned as a python array.
  
Line 13: Line 12:
 
</source>
 
</source>
  
−
===USER EXAMPLES/COMMENTS===
+
===USER COMMENTS===
−
[[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.
+
See [[Rms]] for selection caveats for this group of commands.
−
 
 
−
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]], [[Rms_Cur]], [[Intra_Fit]], [[Intra_Rms_Cur]], [[Pair_Fit]]
+
[[Fit]], [[Rms]], [[Rms_Cur]], [[Intra_Fit]], [[Intra_Rms_Cur]], [[Pair_Fit]]
  
 
[[Category:Commands|Intra Rms]]
 
[[Category:Commands|Intra Rms]]
 
[[Category:States|Intra Rms]]
 
[[Category:States|Intra Rms]]
 
[[Category:Structure_Alignment|Intra Rms]]
 
[[Category:Structure_Alignment|Intra Rms]]

Latest revision as of 05:52, 20 November 2013

intra_rms calculates rms fit values for all states of an object over an atom selection relative to the indicated state. Coordinates are left unchanged. The rms values are returned as a python array.

PYMOL API

cmd.intra_rms( string selection, int state)

PYTHON EXAMPLE

from pymol import cmd
rms = cmd.intra_rms("(name ca)",1)

USER COMMENTS

See Rms for selection caveats for this group of commands.

SEE ALSO

Fit, Rms, Rms_Cur, Intra_Fit, Intra_Rms_Cur, Pair_Fit

Retrieved from "http://pymolwiki.org/index.php?title=Intra_rms&oldid=11476"