Difference between revisions of "Intra rms"

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(remove example (it did not work properly and was actually not an intra_rms example...))
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'''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.
  
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rms = cmd.intra_rms("(name ca)",1)
 
rms = cmd.intra_rms("(name ca)",1)
 
</source>
 
</source>
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===USER EXAMPLES/COMMENTS===
 
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[[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.
 
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I tried made two selections A, and D as
 
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PyMOL>sel A, 1gh2 and n. CA and i. 65-99
 
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Selector: selection "A" defined with 35 atoms.
 
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PyMOL>sel D, 1kao and n. CA and i. 64-98
 
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Selector: selection "D" defined with 35 atoms
 
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which as you can see both yield 35 atoms.  Now,
 
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rms_cur A, D
 
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won't work, due to the aforementioned reason.  To fix this, one needs to do,
 
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alter all,segi=""
 
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alter all,chain=""
 
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alter D, resi=str(int(resi)+1)  # I don't actually use this line
 
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and now
 
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rms_cur A, D
 
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should work.
 
  
 
===SEE ALSO===
 
===SEE ALSO===
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  [[Fit]], [[Rms]], [[Rms_Cur]], [[Intra_Fit]], [[Intra_Rms_Cur]], [[Pair_Fit]]
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[[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]]

Revision as of 18:42, 5 January 2012

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)

SEE ALSO

Fit, Rms, Rms_Cur, Intra_Fit, Intra_Rms_Cur, Pair_Fit

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