Re: [Jmol-developers] Question about coordinates in Jmol
If you are doing this in JavaScript, I would grab the state script and strip out the isosurface command from it that was used (we could add some comments to define it's first and last lines exactly), change the ID, and then run it as an inline script; if doing this in Java, you have access to any particular isosurface's full script command via viewer.getShapeProperty(...). On Tue, Jul 5, 2011 at 9:45 AM, Jonathan Gutow gu...@uwosh.edu wrote: OK, I'll stick with making a duplicate surface. Send me any brainwaves you have on doing this efficiently. For now, I intend to use the original creation command and just switch to translucent mesh for the display mode. 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 -- 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 -- 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
Re: [Jmol-developers] Question about coordinates in Jmol
On Jul 2, 2011, at 2:36 AM, Robert Hanson wrote: Yes, the bounding box is in molecular coordinates. So except for the ghosting -- which I actually do think is done best by displaying two surfaces -- that's no problem with the applet, because you can just deliver it any way you want to. I suggest doing them in two different frames, but you wouldn't have to do that. Great! That's the info I need. One less possibility for changing coordinates to worry about. So the isosurface slab plane does precisely what you are looking for. Both slab and depth are possible. Also, you might want to play around with zshading. That can produce a very nice effect. 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. However, the problem then is that you really don't have full control over the two colors. Having two surfaces should display just as fast -- actually, faster, because you don't have to switch colors in between passes. If we did the ghost thing, we would have to run through all the colixes and reset them on the fly. Could be done but not trivially. Also, this will not reproduce in PovRAY, I think. (Have to think about that; maybe it will.) OK, I'll stick with making a duplicate surface. Send me any brainwaves you have on doing this efficiently. For now, I intend to use the original creation command and just switch to translucent mesh for the display mode. 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
Re: [Jmol-developers] Question about coordinates in Jmol
On Thu, Jun 30, 2011 at 8:50 AM, Jonathan Gutow gu...@uwosh.edu wrote: So I am still at my original question, which is will the boundbox coordinates always be parallel to the molecular coordinates? Yes, the bounding box is in molecular coordinates. So except for the ghosting -- which I actually do think is done best by displaying two surfaces -- that's no problem with the applet, because you can just deliver it any way you want to. I suggest doing them in two different frames, but you wouldn't have to do that. So the isosurface slab plane does precisely what you are looking for. Both slab and depth are possible. Also, you might want to play around with zshading. That can produce a very nice effect. 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. However, the problem then is that you really don't have full control over the two colors. Having two surfaces should display just as fast -- actually, faster, because you don't have to switch colors in between passes. If we did the ghost thing, we would have to run through all the colixes and reset them on the fly. Could be done but not trivially. Also, this will not reproduce in PovRAY, I think. (Have to think about that; maybe it will.) Anyway, sounds great. Bob Jonathan Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX: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 -- 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 -- 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
Re: [Jmol-developers] Question about coordinates in Jmol
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)? Q: Does the slab change when you rotate the model, or is it fixed? (Basically the same as the previous question.) Q: What functionality does this add that does not already exist in the other commands? 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. 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.) 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 On Wed, Jun 29, 2011 at 3:39 PM, Jonathan Gutow gu...@uwosh.edu wrote: As I am working on figuring out what I have to track for a GUI to control slabbing/slicing, I have encountered the issue that the coordinate system for the molecule and the viewing space are not always the same. Do I have to worry about relative rotations of these axes or just the offset of the center? All the examples I've found so far have the origins translated versus each other, but no relative rotations. I'm also trolling the code, but if somebody knows the answer that will save me time. Thanks, Jonathan Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX: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 -- 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 -- 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
Re: [Jmol-developers] Question about coordinates in Jmol
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... ... to do that might be to set a flag to render the translucent pass without slab and the opaque one with. Something on that order would be way preferable to creating a whole new object just for that. Bob -- 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
Re: [Jmol-developers] Question about coordinates in Jmol
Last comment first. On Jun 30, 2011, at 1:10 AM, Robert Hanson wrote: 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... ... to do that might be to set a flag to render the translucent pass without slab and the opaque one with. Something on that order would be way preferable to creating a whole new object just for that. That might be good. It certainly would help with memory. The only issue I see with this option is need for another separate control of the ghost rendering (mostly I think mesh versus fill and level of transparency). What people have been doing is rendering two surfaces one opaque and slabbed and then a ghost unslabbed. In playing around with orbitals and cavities where you may want to see the inside surfaces of the slice through the ghost, I've found that the ghost settings that seems to work best are a transparecy of ~200 and mesh nofill. However, most of the SageMath people have been using filled. The math people also have a tendency to use a different color for the ghost. I'm partial to the same surface color rendering/mapping as the slabbed region. Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX: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
Re: [Jmol-developers] Question about coordinates in Jmol
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 Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX: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
[Jmol-developers] Question about coordinates in Jmol
As I am working on figuring out what I have to track for a GUI to control slabbing/slicing, I have encountered the issue that the coordinate system for the molecule and the viewing space are not always the same. Do I have to worry about relative rotations of these axes or just the offset of the center? All the examples I've found so far have the origins translated versus each other, but no relative rotations. I'm also trolling the code, but if somebody knows the answer that will save me time. Thanks, Jonathan Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX: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
