Marvin FAQ

1. Which files are required to run Marvin applets?
2. How can I create a jar file that contains all necessary classes for Marvin applets?
3. I got a java.util.zip.ZipException exception when I ran a downloaded jar file.
4. How can I set the Java environment of Netscape in Linux?
5. How can I delete plugin packages from the Marvin applets package?
6. How can I create an unsigned jar file from a signed jar file?
7. IE can not load Marvin applets over SSL communication. I have got this warning message: "This page contains both secure and nonsecure items."

To see further questions, visit the following pages:

• Marvin Developer's FAQ (Marvin Beans)
• Crashes, freezes and other bugs FAQ
• Notes for Mac users.

1. Which files are required to run Marvin applets?

   Several packages can be downloaded from the Marvin site:

   • marvin-bin-3.3.2.tar.gz or marvin-bin-3.3.2.zip

     Download and unpack:

     zip: unzip marvin-all-3.3.2.zip
     tar.gz: gunzip < marvin-all-3.3.2.tar.gz |tar xf -

     This distribution contains all files necessary for using MarvinSketch and MarvinView applets, without HTML pages and examples.

   • marvin-all-3.3.2.tar.gz and marvin-all-3.3.2.zip

     Download and unpack:

     zip: unzip marvin-all-3.3.2.zip
     tar.gz: gunzip < marvin-all-3.3.2.tar.gz | tar xf -

     This distribution contains all files necessary for using MarvinSketch and MarvinView applets, as well as the documentation and examples.

2. How can I create a jar file that contains all necessary classes for Marvin applets?

   • Create marvin.jar
   1. Download and unpack marvin-bin-3.3.2.tar.gz or marvin-bin-3.3.2.zip.
   2. Create a new directory: marvintmp
   3. Copy the chemaxon directory and marvin.jar into marvintmp .

   4. cd marvintmp

   5. Unzip marvin.jar .
   6. Create a new jar file:

      zip marvin.jar chemaxon/ *.class

   The new marvin.jar file will contain the required modules for the AWT version of Marvin applets.
   • Create jmarvin.jar

     The following jar files should not be modified because they are signed jars. If you do so, the modified jar is no longer signed.

     1. Download and unpack marvin-bin-3.3.2.tar.gz or marvin-bin-3.3.2.zip.
     2. Create a new directory: marvintmp
     3. Unzip jmarvin.jar and every jar file from sjars directory and its subdirectories to the new directory:

        	    unzip -o jmarvin.jar -d marvintmp
        	    unzip -o sjars/abbrevgroupexport.jar -d marvintmp
        	    unzip -o sjars/batik-core.jar -d marvintmp
        	    unzip -o sjars/clean2d.jar -d marvintmp
        	    ...
        	    

     4. Change location to the new directory and create a new jar file:

        	    cd marvintmp
        	    zip jmarvin.jar *
        	    

     Note: If you do not need SVG export, sjars/batik-core.jar can be skipped.

3. I got a java.util.zip.ZipException exception when I ran a downloaded jar file.

   Some mozilla-based browsers (e.g. Netscape 4.7) treat .jar files as text files, therefore these files can be corrupted during the downloading process.
   Please download .jar files by right clicking on the file's link and select "save as" (or "save link target as") from the pop up menu.

4. How can I set the Java environment of Netscape in Linux?

   Netscape 7.1 / Mozilla 1.4 (and above versions)

   These browsers do not include any Java. They require Java Runtime Environment (JRE) 1.4.2 or later.

   1. If you have not got any Java Runtime Environment on your machine or the installed JRE is not the required version,then download a JRE from the Sun's Java site and install it.
   2. Search the home directory of the browser Most of Linux distributions include Mozilla. Generally, it is located in the /usr/lib/mozilla-X.Y.Z directory (where X.Y.Z is the version number of the browser. E.g.: /usr/lib/mozilla-1.2.1).
   3. Go to the plugin subdirectory of the browser.

      cd <MOZILLA_HOME>/plugin

      Where <MOZILLA_HOME> is the home directory of the browser.
   4. Check your permissions for this directory. Generally, only the administrator (root account) has got a write permission for this directory. If you have got permission problems please consult with your system administrator.
   5. To add Java to the plug-ins list of the browser, you should create a symbolic link to the JRE included Java plug-in.

      ln -s <JRE_HOME>/plugin/i386/ns610-gcc32/libjavaplugin_oji.so libjavaplugin_oji.so

      Where <JRE_HOME> is the home directory of the JRE. E.g.: /usr/java/j2sdk1.4.2/jre
   6. Restart the browser (be sure you have closed each running Netscape or Mozilla applications). Then select Help / About Plug-ins menu item from the menubar to check the available plug-ins in the plug-ins list. If you do not find the required Java plug-in there, exit from the application and restart it again.

   Netscape 6 - 7.02 / Mozilla (1.3.1 and below versions)

   Netscape 6 and Netscape 7.0 contain a built-in Java to run applets. If your browser does not include any Java or you would like set a new default, do the following. (These browsers accept both 1.3.x and java 1.4.x.)

   1. Perform steps 1 to 4 in the previous section.
   2. Create a symbolic link:

          ln -s <JRE_HOME>/plugin/i386/ns600/libjavaplugin_oji.so libjavaplugin_oji.so

      Where <JRE_HOME> is the home directory of the required Java Runtime Environment.
   3. See the 6th step in the previous section.

   In a few cases, the browser can not recognize Java plug-in although you have created the libjavaplugin_oji.so symbolic link in the plugin directory. In that case, add a new symbolic link (libjavaplugin_oji140.so) to the plugin directory. Then restart the browser.

   ln -s <JRE_HOME>/plugin/i386/ns600/libjavaplugin_oji.so libjavaplugin_oji140.so

5. How can I delete plugin packages from the Marvin applets package?

   Remove chemaxon/marvin/plugin and sjars/plugin directories from the marvin directory.

       cd marvin
       rm -r chemaxon/marvin/plugin
       rm -r sjars/plugin
       

6. How can I create an unsigned jar file from a signed jar file?

   Unzip the signed jar file into an empty directory. Delete signing information from the META-INF directory. Finally, create a new jar file with the content of the directory.
   For example creating the unsigned version of the the signed jmarvin.jar file under Linux:

   	unzip -d targetdir jmarvin.jar 
   	cd targetdir
   	rm -f META-INF/CHEMCERT.*
   	zip jmarvin.jar *
       

   Under Linux and Unix, you can run unsigner.sh to unsign signed jar files in Marvin:

   	cd marvin
   	./unsigner -a
       

7. IE can not load Marvin applets over SSL communication. I have got this warning message: "This page contains both secure and nonsecure items."

   The CODEBASE attribute of the OBJECT tag refers to a nonsecure page that the browser does not accept. The browser downloads the plugin from this URL, if the Java Plugin is not installed on your machine.
   You should change this URL to a secure one.
   1. To provide a secure page for downloading a Java Plugin, copy a JRE cab file to your site.

      http://java.sun.com/products/plugin/autodl/jinstall-1_4_2-windows-i586.cab#Version=1,3,0,0
      

   2. Modify the reference to this cab file in marvin.js. (Search the following code in the applet_begin function).

      s += ' CODEBASE=" http://java.sun.com/products/plugin/autodl/jinstall-1_4_2-windows-i586.cab#Version=1,3,0,0"\n';
      

      You should replace the text with

      s += ' CODEBASE=" https://<PLUGINLOCATION>/jinstall-1_4_2-windows-i586.cab#Version=1,3,0,0"\n';
      

      where <PLUGINLOCATION> is the new location of the cab file (e.g.: www.my_secure_site.com/java_plugin). Note: The new URL must start with "https" protocol instead of "http".