View source for Fit

[[Fit]] superimposes the model in the first selection on to the model in the second selection.  Only ''matching atoms'' in both selections will be used for the fit. 

===USAGE===

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

=== ARGUMENTS ===

* '''mobile''' = string: atom selection
* '''target''' = string: atom selection
* '''mobile_state''' = integer: object state {default=0, all states)
* '''target_state''' = integer: object state {default=0, all states)
* '''matchmaker''' = integer: how to match atom pairs {default: 0}
** -1: assume that atoms are stored in the identical order
** 0/1: match based on all atom identifiers (segi,chain,resn,resi,name,alt)
** 2: match based on ID
** 3: match based on rank
** 4: match based on index (same as -1 ?)
* '''cutoff''' = float: outlier rejection cutoff (only if cycles>0) {default: 2.0}
* '''cycles''' = integer: number of cycles in outlier rejection refinement {default: 0}
* '''object''' = string: name of alignment object to create {default: None}

===EXAMPLES===
<source lang="python">
fit ( mutant and name ca ), ( wildtype and name ca )
</source>

If atom identifiers (like segi, chain, ...) in mobile and target do not match, you need to alter them (or use [[Pair_Fit]] instead):

<syntaxhighlight lang="python">
fetch 1a00, async=0
extract hbaA, chain A
extract hbaC, chain C
# hbaA and hbaC are the same protein, but have different chain identifiers
alter hbaC, chain='A'
alter hbaC, segi='A'
# now both have identical atom identifiers
fit hbaC, hbaA
</syntaxhighlight>

===SEE ALSO===
[[Rms]], [[Rms_Cur]], [[Intra_Fit]], [[Intra_Rms]], [[Intra_Rms_Cur]], [[Pair_Fit]]

[[Category:Commands|Fit]]
[[Category:Structure_Alignment|Fit]]