Dear Bob, > Fabulous.
Thanks & sorry for the delay for writting to the list... I took a break ;-) > ps. I don't recommend loading 10 copies of the Jmol applet on a single > page. This crashed the version of Firefox I am using. (Opera was no > problem.) It might be a problem simply because you are using Jmol > 10.2; I can't be sure. I am aware in some conditions the system is unstable. This is particularly true when: - We open two _different_ pages with Jmol applets _in same time_, many browsers we tested simply crash. - Generally, when we open a first time a single page with many applets, it is slow, but it works (in some cases, some molecules do not show up, never the same). When we re-load the page a 2nd, a 3rd time, etc..., the applets show up slower and slower and the system finally crashes... This is true whatever he browsers and their versions... The problem is to be able to get reproductive problems with the Browsers and their many versions, the Jmol versions and the Operating system... We need to work on this, I know. And yes we use a little old version of Jmol. We need to upgrade with the latest version of Jmol. We use mainly Opera, and Firefox and sometimes konqueror (only under linux). We use IE under windows only for testing and because people use windows. > But in general, it's better to have a design > that, for example, supplies a drop-down list, replacing the model in a > single applet. The design idea there is that one can only focus on a > single molecule at any one time anyway -- seeing nine others spinning > is just a distraction. OK thanks. However, when you have a force field topology database (FFTPDB) such as the F-60 project http://q4md-forcefieldtools.org/REDDB/up/F-60/ for instance, it is more informative to display all the fragments in same time. Now, you are right too much is too much ;-) We will release soon bigger FFTPDB with 64, 128 fragments and in this case we will have a huge problem ;-) > Also, I wonder why you want them to spin? The idea was simply: - display the charge values & the structures - display what can be done with Jmol for what we wanted to do > It's impossible to read the > charges that way. You are right, the user can stop the spinning in this case ;-) The applet size is also a little too small... This is once again only for information. If really interested by a project, a user can download the project and study each fragment more specifically using the system he wishes (Jmol, VMD or a program to use the FFTPDB as in CHARMM or AMBER for instance). > How about just loading one molecule at a time and > then displaying the charge distribution using > isosurface molecular map mep For a force field, we were interested to display the _charge values_, themself. Now you are right many other approaches can be applied. Once again, we need to work on this with the new features implemented in the last versions of Jmol... I am particularly interested by the MEP feature available in the lastest versions of Jmol. Thanks for your email: It is great to have feedbacks, comments & criticisms... regards, Francois PS BTW, we do NOT use Tripos mol2 files to display charge values but CML files. These CML files are converted from mol2 files generated by R.E.D. http://q4md-forcefieldtools.org/RED/ using a perl script available @ http://q4md-forcefieldtools.org/Tutorial/0-Script/mol2tocml.pl because of the some problems we encountered: http://q4md-forcefieldtools.org/REDDB/error.php Jmol is described @ http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#18 F.-Y. Dupradeau --- http://q4md-forcefieldtools.org/FyD/ ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
