Align: Difference between revisions
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===USAGE=== | ===USAGE=== | ||
<source lang="python"> | |||
align (source), (target) [,cutoff [,cycles [,gap [,extend \ | align (source), (target) [,cutoff [,cycles [,gap [,extend \ | ||
[,skip [,object [,matrix [, quiet ]]]]]]]] | [,skip [,object [,matrix [, quiet ]]]]]]]] | ||
</source> | |||
===PYMOL API=== | ===PYMOL API=== | ||
<source lang="python"> | |||
cmd.align( string source, string target, float cutoff=2.0, | cmd.align( string source, string target, float cutoff=2.0, | ||
int cycles=2, float gap=-10.0, float extend=-0.5, | int cycles=2, float gap=-10.0, float extend=-0.5, | ||
float extend=-0.5,int skip=0, string object=None, | float extend=-0.5,int skip=0, string object=None, | ||
string matrix="BLOSUM62",int quiet=1 ) | string matrix="BLOSUM62",int quiet=1 ) | ||
</source> | |||
===NOTE=== | ===NOTE=== | ||
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===EXAMPLES=== | ===EXAMPLES=== | ||
<source lang="python"> | |||
align prot1////CA, prot2, object=alignment | align prot1////CA, prot2, object=alignment | ||
</source> | |||
===SEE ALSO=== | ===SEE ALSO=== | ||
Revision as of 13:35, 18 February 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
SEE ALSO
fit, rms, rms_cur, intra_rms, intra_rms_cur, pair_fit