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. So from knowing which bounding box surface faces the wire, the distance to the center of the box is computed readily. The second reason is that it just appears to be easier to establish technically. 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. 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? 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.
Kind regards Martin Hediger ------------------------------------------------------------------------------ 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 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
