On Sun, Feb 9, 2014 at 7:23 AM, Riccardo <[email protected]> wrote:
> Good morning to you, Robert,
>
> For this reason, I'm using Jmol with the option to launch commands from a
> script in silent mode, but there is the problem for java. I asked for java
> to my server hosting, but I thought to upload a portable version of java
> just to launch Jmol for that script (in a linux shell this works, and the
> webserver is based on a linux platform; so, integrating all in a python
> script should be working... I'm testing it).
>
>
Interesting. I've been disappointed by the size of the PDF files (huge!)
when just a simple model is present. BTW, JSmol can also create PDF files,
but I don't have Java source code for converting IDTF to U3D conversion, so
I haven't been able to put those two together and deliver what you are
planning to do from your server.
> *Q*: Among other things, I was looking for a way to insert a command to
> hide the non-polar hydrogens into the Jmol script, but I have not found the
> way; I would also ask for this ... The PyMOL command, for a molecule like
> the pp2 (= CID_4878), would be:
>
> *cmd.hide("(CID_4878 and hydro and (elem c extend 1))")*
>
>
hide _H connected(_C)
should do it.
> Just now, making a google search, I found
> this<http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?_USE=HTML5>page, where
> is a "PyMOL session - dna" example:
>
> *Q*: Probably, is possible to integrate pymol with jmol scripting to hide
> non-polar hydrogens:
> *javascript:Jmol.script(jmolApplet0,'load data/dna.pse')*
> where dna.pse is a PyMOL session file, but probably could be a pymol
> script (.pml) too.
>
>
Jmol can read PSE but not PME.
*Q*: Is it working, or is there something wrong? It seems that I can simply
> replace the previous command in this way:
>
> *<absolute path>/java -jar ./JmolData.jar -o -s <absolute path>/jmol.spt
> -n*
>
> probably, yes. No "-n" option in JmolData. It's headless.
> *R_2*: For this particular script, a Jmol applet (Java or HTML5) is not
> required, for what I said above (I need only to export the idtf file, in
> silent mode, without 3D GUI), because I simply want a form in which the
> user can insert some preferences (like CID molecule, style, etc) to export
> only the pdf.
>
> I see, sure. But it would be more fun for the user to augment and orient
their model as well, don't you think? Note that the TeX file accompanying
the IDTF is what gives the exact orientation and scale. The TeX looks like
this:
\usepackage[3D]{movie15}
\includemovie[
label=t,
autoplay,
repeat=1,
toolbar=false,
3Droo=323.7152,
3Dcoo= 0.0 0.0 0.0,
3Dc2c=0.0 0.0 1.0,
3Daac=16.260204,
% 3Droll=0.0,
3Dbg=0 0 0,
3Dlights=Headlamp,
inline=true,
]{0.9\textwidth}{0.9\textwidth}{t.u3d}
Those 3D settings are the critical part. Unless you know a better way...
> Good to know about the html5 version of Jmol: it works on mobile devices
> too!...
> Only now I see that you are the same author of
> this<http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?_USE=HTML5>web page: I
> sent you an email just now :-)
> It seems that the HTML5 version of Jmol is missing of the idtf exporter...
> so I necessary need of the java version.
>
>
added in http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.8_2014.02.09.zipalong
with VRML, X3D, PovRAY, and (minimal) Maya.
Bob
------------------------------------------------------------------------------
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
