Difference between revisions of "Align"

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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===
Line 19: Line 23:
  
 
===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 14:35, 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