> 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. OK
> - 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. Upon further investigation I have found that RasMol (and the RasMol scripting language) *does* have some support for dealing with multiple models in a PDB file. They use a syntax to specify a specific model number. However, the documentation is *very* sparse and doesn't say much. I will have to do some more investigation. > [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. I understand. It seems to me that it would be straightforward to allow some frames to have more atoms than others. But they would all have to be the same. The other possibility would be to position some atoms far away, and have Jmol ignore them when it is calculating the display scale. Then they would get clipped at rendering time. But that seems quite ugly and bug-prone. I will keep thinking about it. Is there a program which does a *good* job of handling this situation? > So yes, only the positions change (and the connectivity as calculated by > JMOL; b.t.w. can it show double bonds?) Jmol has support for double bonds. For example, .mol files have a connectivity table and double bonds get displayed properly. However, the autobonding mechanism does not currently calculate double bonds. Presumably the algorithm for doing this is implemented in OpenBabel. But frankly, it is low on the priority list right now. > 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....... OK. Currently these charges are not really used by Jmol. Can you send me a very small example of a file with charges so that I can use it to work on charge colors? > 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. This should not be a problem. > 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. Per my other email, I am somewhat concerned about the stability of the Java->JavaScript communications mechanism, particularly on older browsers. But I have not tried it yet. > 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? The JmolApplet can easily load another file from within the same page. > 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. Jmol has mechanisms for measurements. They are available in the applet as well as the application. However, currently there is no gui mechanism to make measurements in the applet. I am trying to figure out what the gestures should be to make measurements. I would rather not change the state to some type of 'measurement mode'. It just causes problems. So I am trying to figure out some type of UI gesture that changes the cursor to a different shape and allows you to make measurements. If you have any suggestions I would appreciate it. > The Weizmann site mentioned by Egon is a nice online version of the > Chime manual. I missed this in Egon's message. I will take another look. > > Well, I think I addressed all the items being raised. If not, please > ask.... Thank you very much. I am traveling today and tomorrow. Will be in touch next week. Miguel > > 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
