Re: [PyMOL] algorithm for alignment

[DeLano S. <de...@de...>]

Linda,

It is not a published algorithm except in the sense that the implementation
is open-source.  In a nutsheel:

"align" does a BLAST-like BLOSUM62-weighted dynamic programming sequence
alignment followed by a series of refinement cycles intended to improve the
fit by eliminating pairing with high relative variability (e.g. >2 standard
deviations from the cycle's mean deviance).

"super" does a sequence-independent structure-based dynamic programming
alignment followed by that same 3D refinement strategy.  

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of Lu Lin
> Sent: Friday, January 25, 2008 4:29 AM
> To: pym...@li...
> Subject: [PyMOL] algorithm for alignment
> 
> Hi all,
> 
> Anyone know which algorithm PyMOL uses to align or super of 
> two structures?
> 
> Thanks a lot!
> 
> Best,
> Linda
> 
> 
> 
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