Difference between revisions of "Intra rms"

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(USER EXAMPLES/COMMENTS)
Line 29: Line 29:
 
  alter all,segi=''
 
  alter all,segi=''
 
  alter all,chain=''
 
  alter all,chain=''
  alter B, resi=str(int(resi)+1)
+
  alter D, resi=str(int(resi)+1) # I don't actually use this line
 
and now
 
and now
 
  rms_cur A, D
 
  rms_cur A, D
 
should work.
 
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]]

Revision as of 10:52, 23 May 2005

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.

PYMOL API

cmd.intra_rms( string selection, int state)

PYTHON EXAMPLE

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

USER EXAMPLES/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.

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, Rms_Cur, Intra_Fit, Intra_Rms_Cur, Pair_Fit