Dear Angel,
Thank you for your reply.
On Thu, 2010-10-28 at 22:09 +0200, Angel Herráez wrote:
> 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)
>
I agree.
> 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.
Yes, that would be nice. But I don't know how to do it. I believe that
Jmol should be recognized as a Firefox plugin as Chime in order to do
so.
>
> > 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
>
Thank you for your confirmation.
>
> > 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
>
Yes, both jmol and jmo.sh call 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.
>
As a standalone program, I hope it can remember the user preferences and
display the structure in the same style/scheme/format every time when
you start the program.
In my case, the original default setting can not show the backbone. I
have to change the style/scheme. Especially, when there are many files
to visualize.
And I just realize that the style/scheme options are not included (or
are hidden some where) in the main menu. Previously, I found the options
by clicking the display window with right mouse key. How could we change
the display style/scheme without using the hidden menu I mentioned?
> > 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.
>
In my opinion, there should be a preference file for each jmol user,
which is stored under user profile folder on Windows system or user home
directory on unix/linux system.
>
> > 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.
>
The "history" and "properties" files under /home/user/.joml/ do store
some settings. For example, the size of display window. I increased the
size of display window before closing the program. I got a display
window with the same size as I adjusted when I restarted the program.
Jmol does remember the window size, why not other settings?
Xiao-Ping
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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
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