On 6/6/06, Bob Hanson <[EMAIL PROTECTED]> wrote: > I'm pretty sure for Eric's sort of animation idea the files would have > all the same atoms, just different coordinates. Is that right, Eric? > It's a molecular system for which the atoms are being moved around. If > bonding has to be updated, that will definitely slow it down, but it > could be an option. > But I don't think the idea is to have different atoms in each frame. Right? >
the particular project i am working on tracks atom movements over long periods of time. i am not a chemist, i want to say it is surface transition theory or something similar. i will let you know and you will probably have an "a-ha" moment. at any rate, though in general the same number of atoms exist between frames, it is possible for them to disappear/reappear, so for my purposes i need to take that in consideration. strangely, though i have been told that jmol is NOT capable of this in animation (frames w/ different numbers of atoms), i have observed that it is. the changes in jmol that would make MY life easier are as follows: - keep only a portion of the animation in memory. it is my understanding that jmol loads the entire animation into memory, making it unsuitable for animations that have, for example, millions of frames. as you mentioned in your response to my original inquiry on this topic so long ago, bob, i feel it is possible for jmol to view an animation much as a word processor views a long document, reading only what is necessary, when necessary. - allow "scripted" animation. by this i mean: if each frame of an animation is stored as a single model in its own file, allow, as input, a list of these files in the order they occur. this is useful for my purposes because it is easy and fast to parse, and the particular sorts of animations i am working with tend to move back and forth over a couple models thousands of times. much easier to include a line of text per frame and two models than thousands of the same model over and over again, as jmol handles animation now. the multiple file loading of jmol 10.x would likely be of key use for this. - enable this sort of functionality for web purposes. ie, download files as needed. this may be beyond the scope of jmol, i'm not sure. > 2) Realize that when multiple files are loaded or any time we have > multiple frames, the atoms are actually in one continuous stream. If you > have 10 models, and each has 15,000 atoms, then you have 150,000 stored > coordinates, frame.atoms[0] - frame.atoms[149999]. in that case i think what i am looking for would set a maximum on this number and refresh the contents of the arrays as needed. > 4) I would recommend not thinking of this as opening a continuous stream > from some huge file, but rather opening specific single-model files and > replacing coordinates model-by-model. Is that compatible with your idea? depends on what you mean. i was wrong earlier when i said that my model deals typically with only a few atoms at a time moving, there is unfortunately no guarantee on how much or little activity i am working with. could you elaborate a bit on this? everything you've sent me so far has been very helpful bob, thanks a lot. i've got your branch checked out and in eclipse and i'll see what i can get out of it today. eric _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
