Align: Difference between revisions
Jump to navigation
Jump to search
mNo edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
===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 12:12, 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