Hens, I have not forgotten about your 'animation' needs.
I have looked some more at the Chime website documentation & the (somewhat obscure) references to PDB NMR in the RasMol documentation. I have determined that the expression evaluation engine will need some restructuring to work properly with multi-frame files ... currently a 'set of atoms' is restricted to a single frame. This needs to change so that a set encompasses all atoms in all frames. Just to set your expectations ... it is going to take some time before I can get to it. I have some other subprojects that are currently higher priority. In addition, this will be a rather big change, so I need to keep thinking about it for some time in order to figure out a restructuring plan. Miguel > 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 -------------------------------------------------- Miguel Howard [EMAIL PROTECTED] c/Pe�a Primera 11-13 esc dcha 6B 37002 Salamanca Espa�a Spain -------------------------------------------------- telefono casa 923 27 10 82 movil 650 52 54 58 -------------------------------------------------- To call from the US dial 9:00 am Pacific US = home 011 34 923 27 10 82 12:00 noon Eastern US = cell 011 34 650 52 54 58 6:00 pm Spain -------------------------------------------------- ------------------------------------------------------- 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
