James,
That actually makes reasonable sense.
On Mon, Jun 25, 2012 at 2:18 PM, James Wonsever <[email protected]> wrote:
> I have been getting some confusing results while trying to use the Load
> "@data" method of loading. Jmol seems to be parsing | and newline
> characters differently.
>
> In the console application, this script command:
>
> mod = '5 \n MolName22Jun2012180152 \n C -0.00025 -0.00025 -0.00025 \n C
> 0.64018 0.64018 0.64018 \n C -0.64075 -0.64075 0.64049 \n C -0.64075
> 0.64049 -0.64075 \n C 0.64049 -0.64075 -0.64075';try{ LOAD '@mod';reset
> mod;}catch(e){}
>
>
Well, let's see. I think this depends upon exactly how you send that to
Jmol.
1) If this is within JavaScript, you will need \\n there:
var script = "mod = '5 \\n MolName22Jun2012180152 \\n C -0.00025 -0.00025
-0.00025 \\n C 0.64018 0.64018 0.64018 \\n C -0.64075 -0.64075 0.64049 \\n
C -0.64075 0.64049 -0.64075 \\n C 0.64049 -0.64075 -0.64075';try{ LOAD
'@mod';reset mod;}catch(e){}"
new way, using JmolApi.js:
Jmol.script(yourAppId, script)
or old way, using Jmol.js:
jmolScript(script, appExtension)
If you are sending it as an initial load script parameter, that can be a
real problem, and you MUST use '|' to separate lines.
With JmolApi.js, you can do this:
jmol = Jmol.getApplet("jmol")
Jmol.script(jmol, script)
just like that, no waiting. With Jmol.js you have to do an
appletReadyCallback to get that script to work with \n on all platforms.
> Will make 5 carbons in a tetrahedral shape, which it is supposed to (I
> think?). It does the same using the Jmol applet on ubuntu using IcedTea
> (firefox and chrome), but the applet fails on windows using sun Java 7.
> (firefox and chrome) Instead, on Windows, it loads 5 unknown (Xx) atoms,
> in a flat plane. I think as a JME format, not XYZ. I want the windows
> version to work the same as the Ubuntu, what do I need to do to make that
> work?
>
>
Possibly. You can tell for sure by looking at the Java console and seeing
what file type Jmol read. I have no idea why the different browsers are
behaving differently there.
> The script:
>
> mod = '5 | MolName22Jun2012180152 | C -0.00025 -0.00025 -0.00025 | C
> 0.64018 0.64018 0.64018 | C -0.64075 -0.64075 0.64049 | C -0.64075 0.64049
> -0.64075 | C 0.64049 -0.64075 -0.64075';try{ LOAD '@mod';reset
> mod;}catch(e){}
>
> Will load a methane molecule on all platforms, this doesn't match the
> input at all. I thought Jmol was supposed to treat pipes and newlines the
> same in this case. If you get rid of the spaces around the pipes, other
> weird things happened.
>
>
You sure you don't have the DATA keyword in there? With DATA Jmol replaces
the "inline character" (default "|") with \n. I'm surprised load '@mod'
does that.
Bob
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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