From: Frieda R. <fr...@ns...> - 2006-03-23 16:27:08
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On Mar 23, 2006, at 12:41 AM, Bob Hanson wrote: > You can also now > set windowCentered OFF Excellent > ]then when you > center (atomno=3) > the molecule rotates around atom 3, but there's no snap. Tested and agreed. > -- Atom 3 isn't put at (150,150) on a 300x300 applet. > An earlier implementation of this was > set frieda ON Is the implementation of 'set windowCentered on/off' the same as 'set frieda on/off'? > but I thought that was somewhat obscene and removed it. Well, I'm not sure I'd agree that it was obscene (although I found it a little strange). But ultimately I decided to be quite honored. :^) >>> But we may need some different or at least explicit mechanism to >>> reset it after spinning, we should add that. >> >> I think this is needed. Let's say that in the context of an >> interactive exercise, I script a spin of the molecule around a >> line, and then stop the spin and expect the student to then rotate >> the structure, do some exploring-- it should rotate sensibly. >> > tell me if it doesn't and we will find a way to make it sensible. Using set windowCentered OFF, this works. There is a small jump due to perspective depth. However, this may become a large jump in a macromolecule... Furthermore, on thinking about applying this command to making movies that focus in on parts of a macromolecule (i.e., you want the molecule to move to, zoom in, and then rotate about the area of interest) the optimal solution to the problem, from my point of view, would be: have Jmol compute the coordinates of a moveTo command that would move the center of a specified atomset to the (XY) center of the applet. You could then center the atomset without fear that there would be any jump. This would mean that you could easily make a smooth transition from a whole-protein view to a close-up of an active site (say) where the active site would now be the center of rotation. Currently I have to do a real dance script-wise to get this to happen smoothly, and it is far from perfect. Is it feasible for Jmol to compute that moveTo? (This request may have a familiar ring to it, especially for Miguel...) >> >> My first approach would be that both points should be specified at >> the same position along the axis that has just been (or is being) >> used for spinning. My intuition says use the midpoint of the line, >> but I am really not sure yet. And I am not sure how to set the >> center of rotation to a point on the line, any suggestions? I will >> look around on the interactive scripting pages and at some of the >> messaging output on your spin test page to see if I can get some >> clues. >> > center $line1 This does work in the sense that the rotation is now about a point on line1, possibly the midpoint - cool! But - big jump. > or possibly > > set windowCentered OFF > center $line1 > > There's bit of a change because of rescaling. In my tests, the still molecule jumps-- not a rescale sort of jump-- much larger, and yet $line1 does not go to the center of the window. In fact, whether windowCentered is on or off has no effect on this jump. Frieda /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// |