Kersten,
Let's talk more about this, can we? I've been thinking, and I suggest that
we might have the basis in Jmol for a very good and very simple model-model
alignment tool. It will take some experimentation, but if you would be
interested in working with me on it, we might have something VERY
interesting (and publishable!) in the end.
Questions:
Q: In the "protein alignment" or "nucleic acid alignment" business, is there
ONE specific method that everyone uses and has decided is THE way to do it,
or is the field open to innovation?
Q: If there is "one way", what is it? How does it work? How is it set up?
Q: What programs do this well?
Q: What programs do NOT do this well -- if there are multiple methods?
Q: Would the Lilley group be interested in collaborating on the development
of new nucleic acid alignment methods?
Bob
On Mon, Mar 8, 2010 at 6:20 PM, Robert Hanson <[email protected]> wrote:
> A suggestion:
>
> If that is all you have, I would suggest pre-aligning. It's easy enough
> with those other programs --- just get the offsets necessary and then apply
> them in Jmol using
>
> translate {some atom list} {x.xxx y.yyy z.zzz}
>
> if you don't want to create all new model files.
>
>
>
> On Mon, Mar 8, 2010 at 8:43 AM, Kersten Schroeder <
> [email protected]> wrote:
>
>> Dear Robert,
>>
>> I really enjoy Jmol and am currently using it on a website I help create
>> for the kink-turn RNA motif (
>> http://www.dundee.ac.uk/biocentre/nasg/kturn/kturns_all.php).
>>
>> Do you plan to develop a way to align model 1 onto model 2 in Jmol script?
>> Pairfit in PyMol does it, so there may be a python code available to help
>> develop in Javascript. I want to align one model (of a list of 30) to
>> another model (of the same list of 30). Therefore, pre-aligning elsewhere
>> would need to be done about 900 times.
>>
>> I look forward to your input. Thank you and have a good day.
>>
>> Kersten Schroeder
>>
>> Kersten Schroeder, Ph.D.
>> MSI/WTB complex,
>> Dow Street,
>> University of Dundee,
>> Dundee DD1 5EH
>> UK
>>
>>
>>
>> ************************************************************
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>>
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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
>
--
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.
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http://p.sf.net/sfu/intel-sw-dev
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