Kersten,
I have had some success in aligning your RNA fragments. Please get back to
me.
Jmol 11.9.34 will align proteins, RNA, and DNA based on quaternion frames
using a new ALIGN command.
See files in
http://chemapps.stolaf.edu/jmol/docs/examples-11/align
for examples.
This is a little different from what you are doing there at your site,
though it is very close. Jmol is aligning the models to give the smallest
standard deviation for a set of quaternions representing the orientations of
the base pairs. As such, it does require prior knowledge of which bases are
to be matched. So the alignment command I used was this:
load files "t1.pdb" "t2.pdb"
frame *
color group
set quaternionFrame "C"
qset1 = quaternion({41-46/1.1}) + quaternion({27-31/2.1})
qset2 = quaternion({77-82/2.1}) + quaternion({92-100/2.1})
align {2.1} {1.1} @qset2 @qset1
Where t1 and t2 are the starting files you have there for at
http://www.dundee.ac.uk/biocentre/nasg/kturn/sites/U4kturnSite.html
Let me explain what this is doing:
First, both files are loaded.
The quaternionFrame "C" setting tells Jmol you want to align based on
nucleic acid bases. Another option is quaternionFrame "P", which aligns
based on the orientations of the tetrahedral phosphorus. But the standard
deviation was somewhat higher for that when I tried it.
qset1 and qset2 are each sets of quaternions. I only have preliminary
manuscripts on how these are set up, but the basic idea is that there is a
little xyz axis set (a "quaternion frame") on each base. You can display
those using:
select *
frame 1
draw quaternions
frame 2
draw quaternions
frame *
Jmol is optimizing the relative orientation of these quaternion frames.
I have to do the concatenation business because the ordering of atoms in the
files are reversed for the two chains -- we need to match bases 77-82 and
92-100 in aligned_to_Kt7/3CC2_HmKt7.pdb (t2.pdb) with bases 41-46 and 27-31
in aligned_to_Kt7/1E7K_U4kt.pdb (t1.pdb), respectively.
I could have left that out and just done
align {2.1} {1.1}
if these had instead been in sequential order.
The ALIGN command then aligns model 2 with model 1 by first finding the
optimum rotation to align the bases based on these quaternion sets, then
doing a simple center-of-geometry translation. It uses a very fast and
robust but rather new method referred to as the determination of the
"spherical mean" from:
Samuel R. Buss, Jay P.
Fillmore<http://www.informatik.uni-trier.de/%7Eley/db/indices/a-tree/f/Fillmore:Jay_P=.html>:
Spherical averages and applications to spherical splines and interpolation. ACM
Trans. Graph.
20<http://www.informatik.uni-trier.de/%7Eley/db/journals/tog/tog20.html#BussF01>(2):
95-126 (2001)
Of course, whether or not this is an acceptable alignment is questionable.
Certainly it has never been done this way before. Still, there are a lot of
variables here, and I could imagine different ways of going about it. It's
not necessarily as simple as "find the smallest root mean square deviation
for the set of atoms" -- because of course we have purines and pyrimidines
mixed along the chains. So perhaps this is an acceptable way to align the
fragments. It's certainly very fast!
I would argue that Jmol's ALIGN command has given a better alignment of the
bases themselves; your alignment probably better matches exact atom
positions. Only you can decide which is "better."
Some questions:
Q: How important is that Jmol produce EXACTLY the result you show at that
site?
Q: Do you have a reference to the algorithm that is being used by your
software?
Q: Would you like to work with me to make the ALIGN command work better for
your purposes?
The jar files needed for this analysis are for Jmol 11.9.34_dev, in
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
Hope to hear from you soon.
Bob
On Mon, Mar 8, 2010 at 9:43 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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--
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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