That's probably not related to the issue you reported, but this part of the js
might have performance issues :
function build_interface(resp)
{
/*
Handling of Q_tot coming from bio_rho.cgi.
Json does not work right now, probably problem on
CGI side:
var q_tot = jQuery.parseJSON(resp);
*/
// Q_tot evaluation.
var q_tot = resp.split(';')[0].split('=')[1];
$('#pHLab').html("Q<sub>tot</sub>at pH " + pH + ": " + q_tot);
// Charge distribution evaluation.
var pqr = resp.split(';')[1].split('=')[1];
$('#pqr').attr("value", pqr);
// Charge distribution.
jmolScript('load pqr::' + pdb_base_path +
'%s-reo.pqr'.replace('%s', target+'-'+pHPad.split('\n')[0]));
jmolScript('select 1.1');
jmolScript('set propertycolorscheme "rwb"');
jmolScript('color property partialcharge');
jmolScript('spacefill 100%');
// Protein representation.
jmolScript('load APPEND ' + pdb_base_path +
'%s-reo.pdb'.replace('%s', target));
jmolScript('select 2.1');
jmolScript('ribbons only');
// NW representation.
jmolScript('load APPEND ' + pdb_base_path +
'nw_%s.xyz'.replace('%s', target));
jmolScript('select 3.1');
jmolScript('spacefill 20%');
// Display configuration.
jmolScript('select 1.1 or 2.1');
jmolScript('set allowRotateSelected');
jmolScript('set dragSelected');
jmolScript('frame *');
// Report Jmol setup finished.
cr();
}
You should reduce the successive jmolScript calls to a single one, with
distinct commands separated by semi-colons.
jmolScript function does many things before actually sending the script to the
applet. The applet is more efficient at dealing
with a script.
Paul
Le 21 juin 2012 à 20:32, Martin Hediger a écrit :
> Dear Jmol Developers
> The next version of our application is almost ready.
> http://www.biofetsim.org/ku_prototype.html
>
> All features we want are in place, now we're basically debugging it and
> cleaning it up.
> One bug which is difficult for me to track down is the following: you'll
> notice a "pH Response" button on the page, which calls a server-side
> application to compute a pH dependent signal of a protein on a
> biosensor. This is dependent on the orientation of the biomolecule in
> the Jmol applet. However, after rotating the molecule, the plot is only
> updated once I click "pH Response" twice. What could be the problem?
> Our code base is hosted on Github, find our repository here:
> https://github.com/mzhKU/BioFET-SIM-WEB
>
> Any feedback for the above problem is highly welcomed. I'm happy to
> provide also more details on the technical background of how the whole
> site is setup.
>
> Best regards
> Martin
>
>
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