distance from center of protein to surface is just:
x = distance({protein}.xyz , {surface}.xyz)
where "protein" and "surface" are appropriate defined.
I don't know why you would want to rotate the boundbox. Do you really need
that at all?
Rotating the protein 90 degrees about the x axis (of the stationary
surface), for example, would be:
select protein
rotateSelected internal {protein} x 90
If you want to rotate about the axes defined by the protein, then that's a
bit trickier and will require some quaternions.
Bob
On Thu, Jun 23, 2011 at 11:08 AM, Martin Hediger <[email protected]> wrote:
> **
> 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} # 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]> 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
>
>
> ------------------------------------------------------------------------------
> EditLive Enterprise is the world's most technically advanced content
> authoring tool. Experience the power of Track Changes, Inline Image
> Editing and ensure content is compliant with Accessibility
> Checking.http://p.sf.net/sfu/ephox-dev2dev
>
>
> _______________________________________________
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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
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