Having just joined the list, I've started to browse the list archives to get a feel for what's interesting in the Jmol world. I came across a discussion on the jmol-developer's list about the desirability of writing animated graphics images, and a request for feedback on how useful that would be (http://sourceforge.net/mailarchive/message.php?msg_id=37619294).
Here are my thoughts (as a user). For some time we've used RasMol to create animated gifs that act as the cover image of our electronic journals (e.g. Acta F, http://journals.iucr.org/f/journalhomepage.html) Why animated graphics as opposed to Jmol-style plugins? 1. For quasi-cosmetic purposes such as journal covers (where the image is small) they are small and fast to load. 2. The journal editors choose the issue's picture from a gallery of candidates - again, it's faster to load up 200 thumbnails on a page than to fire up 200 applets, and I imagine it demands less memory from the browser. 3. Support for legacy browsers: there is a long tail of older browsers, in which animated gifs do at least work. 4. Privacy/memory footprint: users may have disabled Java and/or javascript. We're now introducing Jmol plug-in visualizations, but only as supplementary items because there's no guarantee that all users will be able to use them. Why animated gifs and not, say, animated PNGs? 1. Primarily, support for legacy browsers. 2. Coupled with that, uncertainty as to what (if any) browser support there is for animated PNG formats: I'll be happy to hear other people's experience of this. Note that PNG output from the visualization engine is quite OK; we convert individual PNG images to gifs and merge them to create an animation using standard ImageMagick tools. Our requirement is to create several hundred candidate images in a month, with next to no manual intervention. We therefore have standard scripts which produce 36 frames, separated by 10 degree y-rotation increments, using a fairly vanilla RasMol script that reads an input CIF. Since RasMol's grasp of crystallography is poor, many of the resulting visualizations are unacceptable, but we simply discard them as candidates for the journal cover illustration. Now I'm starting to experiment with Jmol to see whether we can produce better-quality visualizations with default scripts. Given Jmol's greater abilities, I'm thinking of doing a little preanalysis of the structure and loading the most appropriate of a series of default scripts - i.e. a polyhedral view of the unit-cell contents for an inorganic compound, single asymmetric unit for a metal-organic complex etc. No idea yet how far one will be able to get on autopilot, but it will be a fun project. The one gremlin I've stumbled across so far is that I tried to write ouput PNGs of a particular size using Jmol in "blackbox" script mode, i.e. jmol.sh -g 560x450 -ion -s jmolscript -w J90.png is supposed to write an output PNG file 560x450 pixels in extent. I find that it doesn't - my output PNGs are 514x617 pixels. (If I fire up Jmol without the nodisplay flag and manually export the view as a PNG, I get the desired image size OK.) This buglet is not the end of the world, since I can scale and crop as required with ImageMagick, but if there is a quick fix before the full release of Jmol 11.0, that would be great. Given this "blackbox" approach, we can effectively create the animated graphics files we need by careful scripting and postprocessing of the output frames, so the lack of facilities *within* Jmol to export an animated gif (or PNG) aren't a serious obstacle. However, there is a performance penalty in firing up Jmol 36 times per full cycle of rotations, so in that sense the possibility of exporting full animations - provided it can be fully scripted - does have an appeal. Best regards Brian _________________________________________________________________________ Brian McMahon tel: +44 1244 342878 Research and Development Officer fax: +44 1244 314888 International Union of Crystallography e-mail: [EMAIL PROTECTED] 5 Abbey Square, Chester CH1 2HU, England [EMAIL PROTECTED] ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
