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Align
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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