Dear List
I have posted a picture of the system I obtained onto my blog:
http://qmviews.blogspot.com/2011/06/jmol-002-control-over-two-structures.html
A protein structure is placed above a surface of atoms, this is on a
website that is in development.
How can I have a boundbox only around the protein?
Also, assuming the protein/box could only be rotated by 90° around x,y,z
(with some button), I guess I require to introduce a second coordinate
system only for the box, so I know which face of the protein is oriented
towards the surface (this would then be entered into the interface for
further processing). How would I do this?
The whole purpose of this is to find the distance of the center of
bounding box from the surface, which of course is half the side length.
The question is how to figure out which side length to consider.
Any hints are greatly appreciated.
Martin
On 15.06.11 15:32, Robert Hanson wrote:
Depends how you define "surface." If you mean "some other group of
atoms" then you can easily compute that at any time and even display
it real time. If you mean "isosurface" that, too, might be able to be
done, but I might have to add something to make that work.
By "rotatable" I presume you mean independently of that surface.
That's not a problem, and translation is part of it. You just use:
select protein
set allowRotateSelected TRUE
set dragSelected TRUE
Now you can use ALT-SHIFT-LEFT and ALT-LEFT to translate and rotate
the protein relative to the underlying surface atoms.
Now, say you want to update something as that happens. You will need
to use the latest development version of Jmol, because what I describe
next is not in Jmol 12.0. We have a callback called
"atomMovedCallback" that can send a message either to Jmol or to your
page JavaScript to do something. In this case it would report the
distance of "atomX" to the nearest atom of "surfaceAtoms" where you
have already defined them as, perhaps:
atomX = {22.ca <http://22.ca>} # CA for residue 22
surfaceAtoms = {not protein}
select protein
set echo top left
set atomMovedCallback "jmolScript:checkDistance"
function checkDistance() {
Var dmin = 1e10
for (Var x in {surfaceAtoms}) {
Var d = x.distance(atomX)
if (d < dmin) { dmin = d }
}
Var s = format("%3.1f Angstroms", dmin)
echo @s
}
Something like that!
Bob Hanson
On Wed, Jun 15, 2011 at 7:13 AM, Martin Hediger <[email protected]
<mailto:[email protected]>> wrote:
Dear Jmol Users, I'm new to the Jmol list, I'm looking forward to
a nice
community interaction.
I would like to implement the following on a website:
A protein structure should be displayed and it should be rotatable by
the user. At the same time, the distance between a given point in the
structure (e.g. a residue alpha-C atom) and a surface "below" the
structure should be computable (once the structure is oriented the way
it should be. The background is that we want to model a binding
event of
a protein on a nanowire surface, so the orientation of the molecule is
critical.
How could I achieve this?
Kind regards and thank you for answers.
Martin
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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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