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===DESCRIPTION===
===DESCRIPTION===
"align" performs a sequence alignment followed by a structural
'''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.
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 \
align (source), (target) [,cutoff [,cycles [,gap [,extend \
      [,skip [,object [,matrix [, quiet ]]]]]]]]
      [,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,
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>
</source>


===NOTE===
===NOTE===
If object is not None, then align will create an object which
If object is not None, then align will create an object which indicates which atoms were paired between the two structures
indicates which atoms were paired between the two structures


===EXAMPLES===
===EXAMPLES===
<source lang="python">
<source lang="python">
align  prot1////CA, prot2, object=alignment
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]]
[[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

SEE ALSO

fit, rms, rms_cur, intra_rms, intra_rms_cur, pair_fit