Difference between revisions of "Rms cur"

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[[rms_cur]] computes the RMS difference between two atom selections without performing any fitting.
  
[[Rms_Cur]] computes the RMS difference between two atom selections without performing any fitting.
+
By default, only matching atoms in both selections will be used for the fit (same chain, residue number, atoms names etc.). Alternate location mess up the match!
  
===USAGE===
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== Usage ==
<source lang="python">
 
rms_cur (selection), (selection)
 
</source>
 
  
===USER EXAMPLES===
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rms_cur mobile, target [, mobile_state [, target_state [, quiet [, matchmaker [, cutoff [, cycles [, object ]]]]]]]
  
===USER COMMENTS===
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== Arguments ==
See [[Rms]] for selection caveats for this group of commands.
 
  
===SEE ALSO===
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See [[fit]].
[[Fit]], [[Rms]], [[Intra_Fit]], [[Intra_Rms]], [[Intra_Rms_Cur]], [[Pair_Fit]]   
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== Examples ==
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=== Example 1: Identical Identifiers ===
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Alternate location mess up the match, so remove them first.
 +
 
 +
fetch 1p36 1kw7, async=0
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remove not alt ""+"A"
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rms_cur 1p36, 1kw7
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=== Example 2: Homologues ===
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Use [[align]] or [[super]] to create an alignment object (without fitting) and then use the alignment object in the atom selection and turn off identifier matching with '''matchmaker=-1'''.
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 +
fetch 1oky 1t46, async=0
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 +
# create alignment object
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align 1oky, 1t46, cycles=0, transform=0, object=aln
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# RMSD of alignment object
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rms_cur 1oky & aln, 1t46 & aln, matchmaker=-1
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== See Also ==
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* [[align]]
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* [[fit]]
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* [[rms]]
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* [[intra_fit]]
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* [[intra_rms]]
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* [[intra_rms_cur]]
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* [[pair_fit]]   
  
 
[[Category:Commands|Rms Cur]]
 
[[Category:Commands|Rms Cur]]
 
[[Category:Structure_Alignment|Rms Cur]]
 
[[Category:Structure_Alignment|Rms Cur]]

Latest revision as of 02:09, 4 September 2017

rms_cur computes the RMS difference between two atom selections without performing any fitting.

By default, only matching atoms in both selections will be used for the fit (same chain, residue number, atoms names etc.). Alternate location mess up the match!

Usage

rms_cur mobile, target [, mobile_state [, target_state [, quiet [, matchmaker [, cutoff [, cycles [, object ]]]]]]]

Arguments

See fit.

Examples

Example 1: Identical Identifiers

Alternate location mess up the match, so remove them first.

fetch 1p36 1kw7, async=0
remove not alt ""+"A"
rms_cur 1p36, 1kw7

Example 2: Homologues

Use align or super to create an alignment object (without fitting) and then use the alignment object in the atom selection and turn off identifier matching with matchmaker=-1.

fetch 1oky 1t46, async=0

# create alignment object
align 1oky, 1t46, cycles=0, transform=0, object=aln

# RMSD of alignment object
rms_cur 1oky & aln, 1t46 & aln, matchmaker=-1

See Also