Dear Angel,
Yes, your trick (-Djmol.home="$JMOL_HOME" -jar ${JMOL_HOME}/Jmol.jar
"$@" -J trace only) works! I am using "jmol" script, therefore, it looks
like this:
$command -Xmx512m -jar $jarpath $@ -J trace only
That is exactly what I want. Thank you very much! I guess that I can add
other fut
Sorry, make that
$command -Djmol.home="$JMOL_HOME" -jar ${JMOL_HOME}/Jmol.jar "$@" -J trace only
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> 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.
No, Jmol is not a plugin and cannot be. It is an applet, so it can be embedded
in a web page
by the web page author.
It all depends on who contr
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
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 cal
> how bizarre. Is it reproducible on those particular machines?
I didn't have the time to check that. I will report if I can collect the
evidence (not easy for me
these days).
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Hi,
Thank you all for your replies.
I am running Fedora 13 linux system. I would like to use Jmol as a
firefox application to quickly visualize pdb files generated from a
online server (Similar to what rasmol does).
I downloaded Jmol package and uncompressed. I though that I should run
it as
how bizarre. Is it reproducible on those particular machines?
That site uses JmolApplet.jar, so it should be all-inclusive. Can't imagine
what went on there.
Bob
2010/10/28 Angel Herráez
> Hi all
>
> I've had some weird behaviour today while working with my students. Maybe
> some of you
> have
Hi all
I've had some weird behaviour today while working with my students. Maybe some
of you
have seen this before and can give a clue?
We were in a computer room, all PCs configured the same in principle (WinXP in
Spanish).
The students connected to www.pdb.org and clicked on the "View in Jm
Bob said:
> That command works for applet or application.
Good. But if you have to enter it into the console (every day that you open a
page with a
model, or maybe every TIME that the browser opens the Jmol app), then it's
just as easy to
use the menu for changing the style, I guess.
I was t
That command works for applet or application.
2010/10/28 Angel Herráez
> Hi Xiao-Ping
>
> > set defaultLoadScript "trace only"
>
> I think that works for the applet only. Are you using the applet or
> the standalone Jmol application?
> If the second, I think you may need to call a batch or shell
Hi Xiao-Ping
> set defaultLoadScript "trace only"
I think that works for the applet only. Are you using the applet or
the standalone Jmol application?
If the second, I think you may need to call a batch or shell script
file rather than the Jmol.jar directly, so you can insert the "set
defaultL
Dear Xiao-Ping,
set defaultLoadScript "trace only"
(but there are much nicer ways to view a structure!)
http://chemapps.stolaf.edu/jmol/docs
Basically you can do anything in Jmol you ever imagined doing in RasMol and
a few thousand more possibilities.
Lots of examples for how this has been use
Xiao-Ping—there are *tons* of resources available!
The Jmol Website - http://jmol.sourceforge.net/
The Jmol Wiki - http://wiki.jmol.org/index.php/Main_Page
The Interactive Script Documentation - http://chemapps.stolaf.edu/jmol/docs/
If you can't find what you're looking for there, there's always
Hi, jmol-users,
Previously I used rasmol as a web-browser application to open pdb files.
Somehow, when rasmol is open from firefox, it uses 100% power of a
single core CPU/or a core of a multi-core CPU. I decided to use a new
pdb viewer for this purpose. I tried jmol, a very nice tool. But I would
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