Difference between revisions of "Align"

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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,
+
           int skip=0, string object=None, string matrix="BLOSUM62",
          string matrix="BLOSUM62",int quiet=1 )
+
          int quiet=1 )
 
</source>
 
</source>
  

Revision as of 07:42, 30 August 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,
           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