On Tue, Jun 28, 2011 at 4:26 PM, Martin Hediger <[email protected]> wrote:
> The first reason is that we approximate the charge distribution in the
> protein (for the moment) by a point charge at the center of the bounding
> box. Since the proteins we are aiming at (avidine, streptavidine) are
> symmetric tetramers, the distance of the point charge to the surface can
> be approximated by half the length of the bounding box side normal to
> the bounding box surface which is facing the nanowire surface.
>
Sure, but the bounding box:
boundbox {protein}
can be recalculated any time from any rotation or position.
I just keep thinking you don't realize the power of Jmol to do way more than
you are suggesting. It would be way easier, and surely more interesting to
just let the user move the protein around.
> So from
> knowing which bounding box surface faces the wire, the distance to the
> center of the box is computed readily.
>
Right, but that's true any time. As I said, from any position, any rotation,
the center of the
protein can be calculated trivially.
Var centerOfProtein = {protein).xyz
I guess I don't know, but if your surface is laid out nicely, in the x-y
plane, then
Var distanceToSurfaceCenter = {protein}.z - {surface}.z
or, to the top of the surface:
Var distanceToSurfaceTop = {protein}.z - {surface}.z.max
Does it have to be to a specific atom on the surface?
Am I missing something?
> The second reason is that it just appears to be easier to establish
> technically.
I can't imagine why. What you have been describing is far more difficult, I
think.
> Since the charge carriers in proteins are the ionized
> residues, it would require to find the distance of every ionized residue
> to the point on the surface normal below it.
Pretty easy. You mean charged atoms, right? Do you know which ones they are?
Then that is just
Var arrayOfDistances = {protein and partialCharge !=
0}.z.all.sub({surface}.z)
Or, if you wanted to sum distance * charge:
Var sz = {surface}.z
Var distanceTimesChargeArray = for(x;{protein};(x.z - sz)*x.partialCharge)
etc....
> I'm not sure how to do that
> at the moment, you gave me a hint on the "distance" function in Jmol,
> but it requires that I can provide it with the correct arguments. The
> charge carrier is ok to figure out, but how to find the corresponding
> point on the surface?
>
Just align your surface parallel to the xy plane.
Seriously, what you describe can all be done almost trivially in Jmol.
> But it is true, as soon as possible we want to start implement the
> option to freely orient the protein, the problem stated above will then
> need to be addressed.
> Any suggestions on this would be very welcomed.
>
>
Can you describe what you WISH you could do, if you could do more than you
ever thought Jmol could do?
> Kind regards
> Martin Hediger
>
>
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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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All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
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