Difference between revisions of "Align"
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===DESCRIPTION=== | ===DESCRIPTION=== | ||
| − | + | '''align''' performs a sequence alignment followed by a structural alignment, and then carrys out zero or more cycles of refinement in order to reject structural outliers found during the fit. | |
| − | |||
| − | |||
===USAGE=== | ===USAGE=== | ||
<source lang="python"> | <source lang="python"> | ||
| − | + | align (source), (target) [,cutoff [,cycles [,gap [,extend \ | |
| − | + | [,skip [,object [,matrix [, quiet ]]]]]]]] | |
</source> | </source> | ||
===PYMOL API=== | ===PYMOL API=== | ||
<source lang="python"> | <source lang="python"> | ||
| − | + | cmd.align( string source, string target, float cutoff=2.0, | |
| − | + | int cycles=2, float gap=-10.0, float extend=-0.5, | |
| − | + | float extend=-0.5,int skip=0, string object=None, | |
| − | + | string matrix="BLOSUM62",int quiet=1 ) | |
</source> | </source> | ||
===NOTE=== | ===NOTE=== | ||
| − | + | If object is not None, then align will create an object which indicates which atoms were paired between the two structures | |
| − | |||
===EXAMPLES=== | ===EXAMPLES=== | ||
<source lang="python"> | <source lang="python"> | ||
| − | + | align prot1////CA, prot2, object=alignment | |
</source> | </source> | ||
===SEE ALSO=== | ===SEE ALSO=== | ||
| − | + | [[Cmd fit|fit]], [[Cmd rms|rms]], [[Cmd rms_cur|rms_cur]], [[Cmd intra_rms|intra_rms]], [[Cmd intra_rms_cur|intra_rms_cur]], [[Cmd pair_fit|pair_fit]] | |
[[Category:Commands|align]] | [[Category:Commands|align]] | ||
Revision as of 13:12, 29 June 2005
DESCRIPTION
align performs a sequence alignment followed by a structural alignment, and then carrys out zero or more cycles of refinement in order to reject structural outliers found during the fit.
USAGE
align (source), (target) [,cutoff [,cycles [,gap [,extend \
[,skip [,object [,matrix [, quiet ]]]]]]]]
PYMOL API
cmd.align( string source, string target, float cutoff=2.0,
int cycles=2, float gap=-10.0, float extend=-0.5,
float extend=-0.5,int skip=0, string object=None,
string matrix="BLOSUM62",int quiet=1 )
NOTE
If object is not None, then align will create an object which indicates which atoms were paired between the two structures
EXAMPLES
align prot1////CA, prot2, object=alignment