Re: [Jmol-users] Question Jmol / CGI response

[Paul P. <pau...@ac...>]

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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