We don't have a means of running system commands from within Jmol, so you
can't trigger some other program from it, at least not using a script. I
think your best bet is to use the "headless" version of Jmol -- JmolData.jar
-- which has no graphics startup time to slow you down -- or use the -ions
command flags to run silently, with output, no graphics and a script
command, and auto-exit. Process the script and then just start Jmol again
for your second phase of processing.
What does "after a while" mean?
Bob
On Sat, Mar 12, 2011 at 10:07 AM, Alexander Rose <
[email protected]> wrote:
> Hi,
>
> thanks Paul, but that does not describe exactly what I want to do. Let me
> clarify.
>
> I can start Jmol with
>
> java -jar Jmol.jar -s scriptFileName
>
> and everything in 'scriptFileName' gets executed. However, I want to start
> Jmol, execute some Jmol script, feed the results into some other program and
> then execute some more Jmol script based on the output of the other program.
> When I know all the Jmol script I want to execute before I start Jmol I can
> just put it into one script file, but I have some Jmol script I want to
> execute after Jmol has been running for a while. It seems this is currently
> only possible by manually using the built-in Jmol Script Console but not
> programmatically via the command line.
>
>
> Alex
>
>
> Am 12.03.2011 um 15:22 schrieb Paul Pillot:
>
> Hi,
> have you checked at this webpage : 3.1 Command line
> options<http://wiki.jmol.org/index.php/Jmol_Application#Command_line_options>
> on
> Jmol wiki ?
> As far as I understand from the posts to this list, several users have used
> Jmol that way.
> -Paul
>
> Le 12 mars 2011 à 13:09, Alexander Rose a écrit :
>
> Hi,
>
> is there a way to start the Jmol application and then communicate with it
> via the command line?
>
> I have a series a simple calculations I want to do in Jmol (i.e extracting
> certain atoms) and just starting the application takes about the same time
> as doing the calculations. So I figure I could save some time starting Jmol
> once and then feed commands to the application. However I haven't found a
> way. Is this currently possible?
>
>
> Best
> Alex
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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