> well, sure. that would be great for me, and I'd like to contribute in > some way to JMol as well. You *will* be making a major contribution with your scripting expertise ... let's see if you can contribute some Java code as well.
> let me know what you have in mind, and what I > would need to do here. I work almost exclusively in OS X, though I > have a windows 2k box. You can work on OSX. A day or two a week I go to the University of Salamanca (here in Spain) and do Jmol development on OS X. > feel free to tap me for any questions or feedback. Will do > I am also in touch > with all sorts of folks in the biochem world, including other > developers, instructors, modelers, publishers, etc. JMol is a project > that could re-ignite the mol vis field for educators, especially > biochemists; I certainly hope so. > for now, most of us are mired in frustration, and busy > writing elaborate work-arounds. I am aware of that. The reason I started working on Jmol is because a friend of mine at the University of Salamanca showed me his Chime pages ... and then proceeded to tell me the history of RasMol -> Chime and express his frustration about the stagnation of Chime over the last few years. > we (meaning Chime users and developers) have > long been gnashing our teeth at the Chime situation. I would love to > see a JMol that could be scripted via javascript, even if it is not > directly via liveconnect (see my side note, below). that is what most > other programs lack, and to me, it is crucial to producing exciting > content that is easy to access and has a wide distribution. The LiveConnect situatio on MacOS X *will* get better. see below > just a side note: Chime runs in windows IE 6, which does not support > liveconnect events. Hmmm ... LiveConnect works great for me (in both directions) on IE 6 ... sounds like this is MDL's problem. > but we can still communicate with the plug-in via > js, using something called IMBIF - immediate-mode button in invisible > frame. essentially, we use js to write a dynamic html page in an > invisible frame (or layer). the page contains a simple html push > button that presses itself as soon as it is written. the button has > the Chime script attached to it via the script parameter, and it sends > it to the Chime instance identified in the target parameter. since we > write this html using js, all of the parameters can be dynamic. for > example, > > <embed > type="application/x-spt" > hidden=true > width=5 > height=5 > button=push > immediate=1 > target="mol" > script= > "select all; > color yellow; > delay 0.5; > color red; > loop" > > of course, this only works in browsers that can load the Chime plug-in > at all, but it is independent of liveconnect. a recent simple example > is the list of 3d computer models at > > <http://www.molvisions.com/community/smi.html> > > something similar might be useful in JMol, via a param tag? My initial impression is ... "God I hope we do not have to resort to something so ugly with Jmol!" But, in fact it *is* rather ingenious and we could easily use a technique like this for MacOS X. (but, see below) >> And, among the Jmol user community, only a couple of users have much >> RasMol/Chime experience. Chime is mainly used by biochemists. To >> date, Jmol hasn't been able to meet the needs of biochemists, so we >> don't yet have any users from that community. >> > let's hope we can change that! this is something biochem instructors > could really use, to the benefit of their students. The reason I initially approached Brian White is because I needed someone from the RasMol/Chime community to take a serious look at Jmol. For example, I posted something about Jmol to the rasmol mailing list in the late spring, asking for testing assistance ... I received no response. >> >> > I have only browsed your site briefly, using Safari on OS X 10.2.8. >> some of it worked "right out of the box", and some of it didn't. >> Arghh ... >> >> As you probably know, none of the browsers on OS X support >> LiveConnect communication between JavaScript and Java. So there is no >> way to drive the applet from JavaScript, and there is no way for the >> applet to launch callbacks. >> > is there a solution? there will be ... read on > how about an activeX control for the applet? activeX won't work. That is more like a plug-in that will only run on specific browsers. > when I last read it, the documentation for N7 indicated it supports > LiveConnect in the same way that NC4 does. but in practice, or > course, it does not. I agree. It seems to work when the moon is in the right phase. > I am not sure how to interpret that - they plan to do so > in the future? or their doc needs to be updated? No, Netscape has dropped MacOS X support. Microsoft has also dropped IE for MacOS X. > in any case, it is > all but useless unless the other browsers adopt it. <sigh> First, just to make clear, the lack of LiveConnect is really *only* a problem on OSX. LiveConnect works fine in major browsers on all other platforms. Earlier you said: "I would love to see a JMol that could be scripted via javascript" You can do that today ... just not on OSX. And jmol implements the majority of RasMol/Chime script commands. Back to the Mac: Going forward, Safari will be the *only* browser on MacOS that uses the Carbon GUI. Safari is based upon the open source Konqueror code. Konqueror on Linux has supported LiveConnect for about a year. Apple *will* implement LiveConnect because they *must* do so. To date, I have not heard Apple say anything about timeframe ... I have been very frustrated with them. Plus, there is a second option which should open up many more doors. To date, the big problem with porting to MacOS X was the GUI ... because Apple created a *better* user interface. It probably is better, but it is also incompatible with everything else. Apple is including an X11 (X-Windows) server in Panther, the next release of OS X. This means that 'traditional unix gui applications' can be easily ported to OS X. Well, among those 'traditional apps' could be web browsers. The X11 server will make it *much* easier to port Mozilla, Konqueror, etc. to the Mac. And I am quite certain that they will do it. These things will take time to develop and stabilize. But I believe the landscape will be different in 6 to 12 months. So, I know it is frustrating for you as a MacOS X user. But I honestly think that relief is in sight. >> Well, the 'biochemistry' aspect of the Jmol project needs someone >> with your level of application experience and expertise. You could >> really help drive things by helping to set priorities and by doing >> some real stress-testing. You have a suite of web applications that >> we can use as a testbed to improve our chime2jmol.pl translation tool >> and confirm compatible script behavior. >> > count me in! Good. I am dying for you to tell me what you think of the demo pages: http://jmol.sf.net/demo You should also download the Jmol source code, build it, and run both the application and the applet. You will probably need help with this, but just ask us for help. - you will need CVS * it is on the developers toolkit cd * doc is at http://cvsbook.red-bean.com/cvsbook.html * save this link in your browser - java sdk * I think it is also on the developers toolkit cd * it will the probably update from apple to 1.4.1 - go to http://jmol.sf.net and click on Project Page - browse around there and find the stuff about 'anonymous cvs access' Just wondering ... How fast is your Mac? And your Win2K box? See ya, Miguel > > regards, > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > <http://www.molvisions.com/> > usa:north carolina:wake forest -------------------------------------------------- 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 sponsored by: Enterprise Linux Forum Conference & Expo The Event For Linux Datacenter Solutions & Strategies in The Enterprise Linux in the Boardroom; in the Front Office; & in the Server Room http://www.enterpriselinuxforum.com _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
