Hello again, Xiao-Ping I think the key is the way you instruct Firefox to invoke Jmol for opening .pdb files.
> I would like to use Jmol as a firefox application I think the proper name for this situation is "use Jmol as a helper application" that is, Firefox downloads the file and then calls Jmol to open it (as it happens e.g. with a .doc file being passed to MS Word) You could consider the alternative approach which is to setup a way to have Jmol inside a webpage that will so open the pdb file inside the browser. But I guess you are in a different setup. > But I have no idea how to start it. I > found "sh jmol.sh" and "sh jmol" work. That's correct, it's the way to do it and it is explained in the Wiki. By the way, we have little info on how to start Jmol in Linux systems, so if you could share your experience by adding that piece of info to the Wiki, it will be very welcome and useful for other users. http://wiki.jmol.org/index.php/Jmol_Application > Copy or link the jmol.sh to /usr/local/bin/jmol. I call jmol > from firefox, it works fine. But this may not be the correct way. I think it is. Particularly if it works! > As http://jmol.sourceforge.net/download/ stated, from file browser, > double click Jmol.jar can also star the program. But I don't know how to > start it from firefox. Well, you are doing it aren't you? jmol.sh calls Jmol.jar > I put "set defaultLoadScript "trace only"" in File -> Console box and > hit enter. Nothing happens. The change is only effective when loading > the second structure. That's the expected behaviour. > If I close Jmol and restart it again, the setting > returned to original default again. It does not matter if I start Jmol > from firefox or somewhere under my home directory (for example .jmol, > there is .jmol folder under home directory!). That's what I was anticipating too. > Do I need to change the > write permissions of the files in the jmol folder? Certainly not. > I would like to know what is the correct way to put the setting and keep > it as default. Or which file in the Jmol folder (or somewhere under my > home directory or under .jmol directory) controls the default > setting. As far as I know, there is no such file. That's what I was wondering in my previous post. > By the way, when I started jmol with "sh jmol.sh" and "sh jmol", I saw > the following text. What the falses mean? Just default seeting? Everything looks OK there. > Under .jmol folder, the properties contains some settings, which could > be changed by "Edit -> Preferences -> ...". Where are the settings for > other things? I don't know that. ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
