problem of viewing structure with marvinview on firefoxlinux

Dear Linux,

For our application (Chimiotheque Nationale : http://chimiotheque-nationale.enscm.fr/), we use marvinsketch as applet for requesting the chemical library and marvinview for viewing the results.

We install Marvin 5.2.3.

 

If we use firefox 3.5.6 on windows machine, we have no problem to see the results even there are 200 results.(very fast under 2 min)

If we use firefox 3 on linux machine (redhat 64 bits), i can't see the results if the number of answer > 5. ( I have "Module is loading  please wait" and no visualization of the 20 structures after 4 min ) . I think on linux, the load of marvin is very slow.

what do you think?

Can you provide us more info about your software environment where MarvinView displaying issue occurs?

- exact Firefox version
- Java plugin architecture (32 or 64bit) and version

Firefox : 3.0.16

Java : jre-6u17-linux-x64-rpm.bin

(I install java 64 bits and I run : ln -s /usr/java/jre1.6.0_17/lib/amd64/libnpjp2.so
/usr/lib64/mozilla/plugins/libnpjp2.so)

Hi,

I had yesterday a similar problem.

After updating from Ubuntu Linux 9.04 to 9.10 the Marvin-Applet did no more load.

Today I removed all sun-java6 software using apt-get remove sun-java6-bin and then

I installed it new with apt-get install sun-java6-bin and apt-get install sun-java6-plugin

Now the Marvin-Applets run as fine as usual :-)

Obviously it was a version problem on my machine.

Regards, Hans-Ulrich

I am using Ubuntu 9.04 (64bit). I have had problem with GNOME interface. Certain Java application windows (not Marvin) have displayed with empty content. Because of it, I have subsituted GNOME window manager to KDE. Since then, all applications displays fine.
So I can imaging Tran-Minh reported issue can be a Java or Firefox specific bug that occurs only in certain configuration.

We have tested Marvin applets under Linux (KDE window manager) with Firefox 3.0.14, Java 1.6.0_16, but we have not find any problem with the applet on that platfom.

I recommend to try out applet with newer Firefox version or with another Java Plugin.

Can you reproduce the problem with any example on ChemAxon site? I recommend to check these examples: http://www.chemaxon.com/jchem/examples/db_search/index.jsp

dear support,

I try : http://www.chemaxon.com/jchem/examples/db_search/index.jsp

and it works on Linux.

 

With my application, If i would like to visualize 20 results, the applet marvin is empty on Linux whereas on Windows, I can see the structures in the applet.

With my application If i have 20 results following a query, 20 applets are loading whereas in the examples : 

http://www.chemaxon.com/jchem/examples/db_search/index.jsp... />
I remark that if there were 20 results, only 1 applet is loading?

I use for viewing the results : 

<script LANGUAGE="JavaScript1.1" SRC="marvin/marvin.js"></script>
<script LANGUAGE="JavaScript1.1">
                                    <!--
// marvin_jvm = "builtin"; // "builtin" or "plugin"
   mview_begin("marvin/", 250, 120); //arguments: codebase, width, height
                                    // you could also use the mview_begin("../../..", 200, 200, true ); function call to load the applet without splash screen.
                                    <?php if ($tabstru[$ligdata[$i]["STRU_ID"]]!='') { ?>
                                    mview_param("mol", "<?php echo $tabstru[$ligdata[$i]["STRU_ID"]];?>");
                                    <?php } ?>
                                    mview_param("molbg", "#ffffff");
                                    mview_param("rendering", "wireframe");
                                    mview_end();
</script>

Oh, I see. So there are 20 applet instances on the same page.

We do not recommend to do this. In this case,  the performance of each applet can decrease drammatically. Furthermore it can cause further performance issues. For example Java can run out of memory because 20 times memory is allocated in this case than normally.

Instead of that, use one applet instance with grid layout. Our jchem examples follow this way.

I also recommend to take a look at to the ajax examples where applets are substituted with images in the table and the cell content where molecule is located is replaced to an applet when click on it.

http://www.chemaxon.com/ajax/

In fact, with Linux my application works well. Before I use cygwin to connect to my Linux server and to the application with marvin. If I try my application directly from the Linux server, the results are well visualized with marvin applet even there are 20 results/page.

Probably, it is a platform specific browser - Java issue. It seems that Java on Linux still handle 20 applets but Windows can not do it. Anyhow, using several applets on the same page decrease the performance that's why we do not recommend this way.