I think I can do it with quaternions in about two lines of Jmol script. Is
there a good reference for Singular Value Decomposition?
Bob
On Wed, Mar 10, 2010 at 2:54 PM, Andreas Prlic <[email protected]> wrote:
> 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
>>
>>
>> ------------------------------------------------------------------------------
>> Download Intel® Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> _______________________________________________
>> Jmol-users mailing list
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>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
_______________________________________________
Jmol-users mailing list
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