[PyMOL] Re2: algorithm for alignment

Dear Warren,

Does the algorithm support flexible alignment? Thanks a lot!

Best regards,
Linda

DeLano Scientific wrote:
> 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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