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 a standalone application. But I have no idea how to start it. I
found "sh jmol.sh" and "sh jmol" work. In order to link it with firefox,
I have to move the folder to /usr/share/jmol and make jmol.sh as an
executable. 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.
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.
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. 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!). Do I need to change the
write permissions of the files in the jmol folder?
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.
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?
useCommandThread: false
JmolConsole is initializing
User macros dir: /home/zhang/.jmol/macros
exists: false
isDirectory: false
Under .jmol folder, the properties contains some settings, which could
be changed by "Edit -> Preferences -> ...". Where are the settings for
other things?
Thank you for your help.
Xiao-Ping
On Thu, 2010-10-28 at 20:04 +0200, Angel Herráez wrote:
> 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
> defaultLoadScript" command.
>
> Please, tell us how you are curently doing the connection from web
> browser to viewer.
>
>
> > complete JMOL user guide or manual freely available?
>
> See
> http://wiki.jmol.org/index.php/Jmol_Tutorials
> http://wiki.jmol.org/index.php/Literature
>
>
>
> ------------------------------------------------------------------------------
> 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
------------------------------------------------------------------------------
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
