Dear Warren,
Thank you for your reply!
Besides, sometimes when I align two structures by their ca atoms, one of
them keeps trembling, do you know why?
Thanks again!
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:del...@delsci.info
-----Original Message-----
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Lu Lin
Sent: Friday, January 25, 2008 4:29 AM
To: pymol-users@lists.sourceforge.net
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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