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.
Andreas
On Wed, Mar 10, 2010 at 8:26 AM, Robert Hanson <[email protected]> wrote:
> 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.
> 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
>
>
------------------------------------------------------------------------------
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
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