Bob,
Yes, I was thinking of something more simplistic. Pair_Fit in PyMol fits a set
of atom pairs between two models. I am aware that people use Xplor-NIH as well
to align models that contain nucleic acids. I am not sure if Xplor-NIH or
Pair_fit in Pymol is a better starting point.
I will be willing to work with you and try to figure out the best way to
proceed with the alignment of models containing nucleic acids. Thank you and
have a good day.
Kersten
>>> Robert Hanson 10/03/10 7:58 PM >>>
I think what I'm thinking of is considerably more simplistic and lessgeneral --
just the ability to specify two sets of atoms and have Jmolalign 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 <andr...@sdsc.edu> wrote:
no, protein only...
On Wed, Mar 10, 2010 at 10:43 AM, Robert Hanson <hans...@stolaf.edu> 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 <andr...@sdsc.edu> 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 forprotein structure alignments. We recently
released it under LGPL aspart of BioJava.
>>> Robert Hanson 10/03/10 4:28 PM >>>
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 <hans...@stolaf.edu> 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 <k.schroe...@dundee.ac.uk>
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
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