Miguel, Egon, and others, To summarize: I know of two type of multiple structure animations that Chime is used for: - the multiple XYZ file, having the same atoms in the same order in every frame. This is the one used for vibrations, conformational changes and reactions of 'organic' molecules. - the multiple PDB file (aka PDB NMR), used by the protein crowd, and of which I don't know exactly what the restrictions are. I assume this is closer to deleting one structure and reading the next. [A third type people call animations involve actually one structure being rotated, zoomed, highlighted etc.] My personal interest is in the mXYZ type. Of course it would nice to be more flexible in the number of atoms. Now, if you show a reaction, all reagents (atoms) have to be present from beginning to end. However, sometimes you would like to introduce a reagent somewhere halfway, e.g. when you need a base to remove a proton. A compromise would be that all atoms are present in all frames, but that certain atoms can be excluded from being displayed in certain frames, get a zero radius or whatever. So yes, only the positions change (and the connectivity as calculated by JMOL; b.t.w. can it show double bonds?) As Egon noted, the mXYZ format can have a charge value in the last column. My experience with Chime is that this value is largely ignored; my impression is that Chime is calculating the charges once and using these (when displaying the electrostatic potential surface) over the whole animation. Something to improve on.......
Then the animation control commands. yes, the number of frames per second should be a variable. In general reactions are shown at a slower rate than conformational changes, as more is changing in the picture. Even better would a dial or slider by which the viewer can change the rate. I already mentioned the frame number that should be returned, to synchronize other actions controled by JavaScript. Like the display of text, or changes in a picture (e.g. an energy diagram) next to the structure. About the other functions: the Chime picture is somewhat troubled because we use the MoI (Method of Interaction, the moiscript.js Egon quoted from) script to make Chime less browser dependent. But what we use/need, in general, not within animations, is the following: PickCallback returns the atom (number, label) being clicked by the user. This we use in our editor, that reads a MOPAC z-matrix input file. The selected atom is being replaced by a substituent (one or more atoms) from a list. A new MOPAC file is written and send to the page. Can this be done in JMol/Java by just redrawing the structure, or by reloading the applet, or by reloading the whole web page as is done now? MessageCallback is used to transfer measurement data like distances, angles and torsions. I think JMol has its own provision for that? The values could be echoed to the status line, but should also be available for JavaScript, to be displayed in a text area on the web page. The Weizmann site mentioned by Egon is a nice online version of the Chime manual. Well, I think I addressed all the items being raised. If not, please ask.... Hens -- Dr. J.H. (Hens) Borkent, CMBI, University of Nijmegen P.O. Box 9010, 6500 GL Nijmegen, The Netherlands Tel 0031 24 3653388 Fax 0031 24 3652977 http://www.cmbi.kun.nl/ Centre for Molecular and Biomolecular Informatics ------------------------------------------------------- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
