I try to answer your questions below. In summary, now that you've changed the isosurface slab command so that it can be done after the surface is defined I am mostly concerned with building a GUI that is intuitive enough that people don't have to understand the details of the isosurface and slab commands to look at a section through the displayed object. My first goal is to get this working well for isosurfaces, but I don't think it will be hard to extend it to do everything.
On Jun 30, 2011, at 1:07 AM, Robert Hanson wrote: > well, the molecular coordinates are just the molecular coordinates. This > "slicing" is by them, right? Not the screen coordinates? There are three > coordinate systems: > > -- molecular coordinates > -- relation of those by rotation to the original view (the orientation > quaternion/matrix) > -- translation of that into screen coordinates (the transformation matrix) > > I'd sure like to hear more about what the specs are going to be on this > "slice" command. Before you go too far, Jonathan, can you remind us of what > exactly it is going to do? > > Q: Are we slicing in molecular coordinates (like isosurface slab plane... and > slab plane...) or screen coordinates (like slab/depth and isosurface slab > nnn)? The first draft will be slicing in molecular coordinates, although I think some people might also like a GUI for slab/depth like behavior. > > Q: Does the slab change when you rotate the model, or is it fixed? (Basically > the same as the previous question.) People wanted to be able to look at the slice from different angles so that's why molecular coordinates. > > Q: What functionality does this add that does not already exist in the other > commands? Other than a ghost feature, which presently requires building a duplicate surface, I cannot think of anything. Anyway, the issue is that people want the ability to specify the slice in a way that is logical relative to the view. Tentatively, I am going to make the controls relative to the origin of the boundingbox. If they are relative to the view orientation, things change on rotation and translation. I think that would be confusing. I think there should also be an option to do everything relative to the absolute coordinates (molecular). I'll just set a switch. So I am still at my original question, which is will the boundbox coordinates always be parallel to the molecular coordinates? > > There is no point in adding a new command unless it makes *scripting* far > easier. This sounds a lot more like a GUI thing -- which would use the > already-existent commands, possibly with a few modifications to suit. I agree. Initially as I began looking at what Jmol could do, I thought it would help. Now I'm not sure. > > It seems to me a popup window is a nice idea -- at least for the application. > Not convinced with respect to the applet -- we don't do that, so far, except > with the signed applet for file read/write. A good dialog can take lots and > lots of code to produce and work with. If possible, with the applet, we > should do that in JavaScript, not Java. (My opinion.) I agree for another usability reason as well. When you have more than one applet on a page it is difficult to tell which one the pop-ups go with. A javascript tool that is anchored on the page in the vicinity of the applet is much easier to understand. That is one of the reasons, I thought about a special command. The idea being that the smaller the scripts that have to be passed the better the potential for speed. > > By the way, you asked about the possibility of duplicating an isosurface so > there was a translucent "shadow." Since rendering is a two-pass system, a > better way I like your idea and have sent a comment in a separate message. Jonathan Dr. Jonathan H. Gutow Chemistry Department gu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow ------------------------------------------------------------------------------ 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-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers