Fit - Revision history

Cchem: 2 revisions

2019-11-24T02:11:53Z

2 revisions

Hongbo zhu: recommend Pair_Fit if atoms do not match

2019-11-12T11:17:42Z

recommend Pair_Fit if atoms do not match

Hongbo zhu: highlight usage caveat

2019-11-12T11:13:23Z

highlight usage caveat

Cchem: 1 revision

2019-04-01T03:11:56Z

1 revision

Speleo3: alter segi

2019-03-07T08:26:57Z

alter segi

Pyadmin: 10 revisions

2014-03-28T01:46:43Z

10 revisions

Speleo3: example

2012-01-05T22:56:33Z

example

Speleo3: matchmaker argument

2012-01-05T22:35:00Z

matchmaker argument

New page

[[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>

===USER COMMENTS===
See [[Intra_Rms]] for selection caveats for this group of commands.

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

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

Vinnyrose at 13:48, 20 June 2009

2009-06-20T13:48:14Z

New page

===DESCRIPTION===
[[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===
<source lang="python">
fit (selection), (target-selection)
</source>

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

===USER COMMENTS===
See [[Intra_Rms]] for selection caveats for this group of commands.

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

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

Cmoad at 17:15, 17 February 2005

2005-02-17T17:15:20Z

@@ Line 1: / Line 1: @@
 [[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===
@@ Line 26: / Line 26: @@
 </source>
-If atom identifiers (like segi, chain, ...) in mobile and target do not match, you need to alter them:
+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">
@@ Line 40: / Line 40: @@
 ===SEE ALSO===
-[[Rms]], [[Rms_Cur]], [[Intra_Fit]], [[Intra_Rms]], [[Intra_Rms_Cur]]
+[[Rms]], [[Rms_Cur]], [[Intra_Fit]], [[Intra_Rms]], [[Intra_Rms_Cur]], [[Pair_Fit]]
 [[Category:Commands|Fit]]
 [[Category:Structure_Alignment|Fit]]

← Older revision		Revision as of 11:13, 12 November 2019
Line 1:		Line 1:
−	[[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.	+	[[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===		===USAGE===

@@ Line 34: / Line 34: @@
 # hbaA and hbaC are the same protein, but have different chain identifiers
 alter hbaC, chain='A'
 # now both have identical atom identifiers
 fit hbaC, hbaA

← Older revision		Revision as of 17:15, 17 February 2005
Line 12:		Line 12:
	===SEE ALSO===		===SEE ALSO===
	[[Cmd rms\|rms]], [[Cmd rms_cur\|rms_cur]], [[Cmd intra_fit\|intra_fit]], [[Cmd intra_rms\|intra_rms]], [[Cmd intra_rms_cur\|intra_rms_cur]]		[[Cmd rms\|rms]], [[Cmd rms_cur\|rms_cur]], [[Cmd intra_fit\|intra_fit]], [[Cmd intra_rms\|intra_rms]], [[Cmd intra_rms_cur\|intra_rms_cur]]
		+
		+	[[Category:Commands\|fit]]

← Older revision	Revision as of 02:11, 24 November 2019
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← Older revision	Revision as of 03:11, 1 April 2019
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← Older revision	Revision as of 01:46, 28 March 2014
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