Difference between revisions of "Fit"
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Hongbo zhu (talk | contribs) m (recommend Pair_Fit if atoms do not match) |
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| − | + | [[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=== | ||
| − | fit | + | |
| + | 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=== | ===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=== | ===SEE ALSO=== | ||
| − | + | [[Rms]], [[Rms_Cur]], [[Intra_Fit]], [[Intra_Rms]], [[Intra_Rms_Cur]], [[Pair_Fit]] | |
| − | [[Category:Commands| | + | [[Category:Commands|Fit]] |
| + | [[Category:Structure_Alignment|Fit]] | ||
Latest revision as of 07:17, 12 November 2019
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
fit ( mutant and name ca ), ( wildtype and name ca )
If atom identifiers (like segi, chain, ...) in mobile and target do not match, you need to alter them (or use Pair_Fit instead):
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