For this you just need e.g. a Singular Value Decomposition ...
Andreas
On Wed, Mar 10, 2010 at 11:57 AM, Robert Hanson <[email protected]> wrote:
> I think what I'm thinking of is considerably more simplistic and less
> general -- just the ability to specify two sets of atoms and have Jmol align
> one set to the other via an optimized rotation and translation.
>
> That's what you are interested in, right Kersten?
>
> Bob
>
> On Wed, Mar 10, 2010 at 12:47 PM, Andreas Prlic <[email protected]> wrote:
>
>> no, protein only...
>>
>>
>> On Wed, Mar 10, 2010 at 10:43 AM, Robert Hanson <[email protected]>wrote:
>>
>>> Ah, that's useful information, Andreas. Does it also work with nucleic
>>> acids?
>>>
>>> On Wed, Mar 10, 2010 at 12:11 PM, Andreas Prlic <[email protected]>wrote:
>>>
>>>> Hi,
>>>>
>>>> We are using Jmol to visualize protein structure alignments as part of
>>>> the RCSB PDB Protein Comparison Tool.
>>>> http://www.rcsb.org/pdb/workbench/workbench.do
>>>>
>>>> It contains the Combinatorial Extension (CE) algorithm (among others),
>>>> which is a frequently used algorithm for protein structure alignments. We
>>>> recently released it under LGPL as part of BioJava.
>>>>
>>>>
>>>>
>>>
>>
>>
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>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
> ------------------------------------------------------------------------------
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------------------------------------------------------------------------------
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Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
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http://p.sf.net/sfu/intel-sw-dev
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