MarvinView and shortcut groups problems

Hi,

Last night I had about 150 students using MarvinSketch and MarvinView 5.2.5.  A small but significant number of students had one or both of the following problems:

• No shortcut groups were available, either by typing their names or through the Insert -> Groups menu.


• When MarvinView was launched, no structure appeared.

Other students, using exactly the same installation, observed no problems.  At least the shortcut groups problem was observed on both Macs and PCs.

Our invocation of MarvinView is as follows:

           <script type="text/javascript">

                mview_name = "ans_applet";

                mview_begin("/nosession/marvin", 350, 350);

                mview_param("preload", "SmilesExport,MolExport,Clean2D,Parity");

                mview_param("mol", mol);

                mview_param("atomMappingVisible", "false");

                mview_param("molbg", "#FFFFFF");

                mview_param("rendering", "wireframe");

                mview_param("valenceErrorVisible", "true");

                mview_end();

            </script>

The code for the compound that, for some students, was not displayed in MarvinView (they saw a blank window):

<?xml version="1.0" ?>

<cml>

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray

          atomID="a1 a2 a3 a4 a5 a6 a7 a8"

          elementType="C C C C C C C Br"

          x3="1.1950689605947398 -0.14447467270219105 -0.8180500754738472 0.2506183413260592 1.489066887587136 2.165353076146937 0.78699152447984 -0.45717701294551283"

          y3="-1.5736032022111694 -2.319125385430205 -2.2917289058477897 -1.5640742776683818 -2.480778995053588 -2.4635548476775124 -0.5013091798092489 -0.8215890038881013"

          z3="-2.440992908853478 -2.703720387973862 -1.3085314499658904 -0.44374579884479914 -0.2220361841423915 -1.615850494611149 -1.4183682962298576 1.1933785118735742"

          />

      <bondArray>

        <bond atomRefs2="a1 a2" order="1" />

        <bond atomRefs2="a2 a3" order="1" />

        <bond atomRefs2="a3 a4" order="1" />

        <bond atomRefs2="a4 a5" order="1" />

        <bond atomRefs2="a5 a6" order="1" />

        <bond atomRefs2="a1 a6" order="1" />

        <bond atomRefs2="a1 a7" order="1" />

        <bond atomRefs2="a4 a7" order="1" />

        <bond atomRefs2="a4 a8" order="1" />

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

I am not able to reproduce these problems on my PC or my two Macs, and there were many students who did not have these problems.

Finally, Rafi also observes that MarvinView does not work in Firefox on his machine.  He says,

mview_begin and msketch_begin are declared twice with different parameter lists.  JavaScript does not recognize such overloading.

Do you have any insights?

-- Bob

I assume it can be a client side issue.

The problem may be caused by the browser or by the Java Plugin.

In first round, I would clear the Java cache.

After then, if the loading issue is still existing, I would check the Java console and JavaScript error dialog. Probably, some error messages have been displayed there. If yes, this message would help a lot to detect the real problem.

There is a class loading bug in Sun Java 1.6.0_15 and in higher versions. If your users use this Java version, this bug can cause the applet loading problem. See linking topic about it:

http://www.chemaxon.com/forum/ftopic5319.html

I can also imagine that it can be a browser issue. Probably, it does not handle properly special characters. Probably, the embedded molecule source into the JavaScript / html code could not be evaluated properly.

As I see, you give the molecule source via the "mol" variable in the applet code:

mview_param("mol", mol);

How you set this variable? Do you encode somehow the mrv source?

Clearing the Java cache solved the problem for most students who have reported back, though not all.  I will see whether the remaining students have Java 1.6.0_15 or greater; if so, I will try your workaround.

Thanks.

I am happy that the problem have been solved by most of your users.