Issues with Delta2D and 3D-representation

The Problem

You are trying to view a 3D-view of a spot from the Dual View (Dual View Menu: Rollups -> 3D Spots), but one of the following happens:

The rollup opens, but is completely blank.

Before you begin to fix the problem of a blank 3D-rollup: Please make sure that the rollup does not correctly present a blank area of your gel image but really should display a spot by clicking somewhere in the Gel image randomly with the Spot Selection Tool of the Dualview.

Please note, that selecting several spots at once does not show the complete area in the 3D rollup, but simply does nothing with the 3D rollup. If you want to view a bigger area than a single spot in a 3D representation, open the Preferences > 3D Spots and check the mark on fixed size. In the nearby textbox you can set the size of area you want to be shown in pixels. Please mind, that the bigger this value is, the more time is needed for computing the representation. Now you can click in the desired area, select several spots and watch them in the 3D Rollup.

The Dual View suddenly dissappears, Delta2D has crashed completely

The underlying Sun Java™ software has problems controlling the installed graphics interface, which can have multiple reasons:

1. The graphics drivers installed on many computers are only the basic drivers offered by the used operating system and were never updated. These drivers mostly lack the advanced functions needed for a 3D-representation.
2. To benefit from the ongoing development of Java, the Java components used in Delta2D are kept up to date. Sometimes it can happen that modifications of certain parts of Java are not or not yet compatible to all graphics drivers.
3. Some computers are equipped with so called "on board graphics chipsets". This is not generally a bad idea, since it saves costs and they do most jobs very well. But sometimes such a chipset lacks abilities needed for 3D representation.
4. Especially for older versions of Microsoft® Windows™ to increase performance users have been advised to modify the settings for the Virtual Memory from system managed size to a fixed custom size. On some computers this seems to affect their abilities of 3D-representation.
5. In one case a user who has replaced a competing software by Delta2D reported that the 3D-Problem has been resolved by uninstalling the competing software. However, in general it will be difficult to locate the problematic software.

Solutions

Please ask your system administrator for help if you have insufficient rights to maintain your system or if you feel uncertain how to deal with the following suggestions.

1. First update your graphics drivers. This already helps in four out of five cases. Background: Delta2D is always shipped with the latest Java 3D components, which require OpenGL in a certain minimum version. For now OpenGL 1.3 has to be supported by your graphics board and its drivers.

   Now Find out if and which Version of OpenGL your Computer Supports

   On a windows system you can use the command line tool wglinfo, under linux you can use the in most cases already available command "glxinfo" to find out, which version of OpenGL is supported by your system. There comes quite a lot of output; simply search (linux: grep) for the string "OpenGL version string:". If this value is not something like '1.2' or '3.0.0', you can be pretty sure that OpenGL will not work. In this case you can directly jump to Using DirectDraw as replacement for OpenGL. If the version reported is lower than the version mentioned above, try the next step.
   
   
2. Downgrade the Java 3D components of your Delta2D installation to an older version. One by one you can try out which Java3D version from the list below can work with the OpenGL version available with your graphics board. Please make sure to try them all before you give up. We already met the weirdest combinations of graphics board and J3D-versions working or not.

   Replacing the Java 3D Component of Delta2D by Older Versions

   The list below offers Java 3D component installation files for Windows 32bit and 64bit, Mac and Linux 32bit and 64bit in descending version sequence. Please note that the topmost version is the one shipped with the current version of Delta2D, so start testing with the second version matching your operating system and proceed with older versions if the tried version does not fix the problem.

   • Quit Delta2D.
   • Download the setup file to your computer.
   • For linux(32+64) only: Make the downloaded file executable: cd to the folder where the downloaded file is saved and type

     chmod u+x Delta2D4_J3D_1_5_2_linux.sh

     (resp. the matching filename)
   • Execute the file by double clicking on it and follow the instructions of the setup wizard.
   • Please make sure to choose the correct installation folder of Delta2D.
   • Start Delta2D.

   Java3D patches for Delta2D 4.x:

   	File		Last Modified	Size
   	Delta2D4_J3D_1_5_2_windows64.exe		April 20, 2009	3.4 MB
   	Delta2D4_J3D_1_5_2_windows.exe		April 20, 2009	3.8 MB
   	Delta2D4_J3D_1_5_2_mac.dmg		April 20, 2009	3.4 MB
   	Delta2D4_J3D_1_5_2_linux64.sh		April 20, 2009	3.0 MB
   	Delta2D4_J3D_1_5_2_linux.sh		April 20, 2009	3.0 MB
   	Delta2D4_J3D_1_4_0_windows.exe		January 28, 2009	3.1 MB
   	Delta2D4_J3D_1_4_0_linux64.sh		January 28, 2009	2.4 MB
   	Delta2D4_J3D_1_4_0_linux.sh		January 28, 2009	2.3 MB
   	Delta2D4_J3D_1_3_2_windows.exe		January 28, 2009	2.9 MB
   	Delta2D4_J3D_1_3_2_linux64.sh		January 28, 2009	2.2 MB
   	Delta2D4_J3D_1_3_2_linux.sh		January 28, 2009	2.2 MB

   Java3D patches for Delta2D 3.x:

   	File		Last Modified	Size
   	Delta2D_J3D_1_5_1_windows64.exe		August 15, 2007	3.1 MB
   	Delta2D_J3D_1_5_1_windows.exe		August 15, 2007	3.5 MB
   	Delta2D_J3D_1_5_1_mac.dmg		August 15, 2007	3.1 MB
   	Delta2D_J3D_1_5_1_linux64.bin		August 15, 2007	2.8 MB
   	Delta2D_J3D_1_5_1_linux.bin		August 15, 2007	2.7 MB
   	Delta2D_J3D_1_4_0_windows.exe		August 15, 2007	2.8 MB
   	Delta2D_J3D_1_4_0_linux64.bin		August 15, 2007	2.1 MB
   	Delta2D_J3D_1_4_0_linux.bin		August 15, 2007	2.1 MB
   	Delta2D_J3D_1_3_2_windows.exe		August 15, 2007	2.6 MB
   	Delta2D_J3D_1_3_2_linux64.bin		August 15, 2007	2.0 MB
   	Delta2D_J3D_1_3_2_linux.bin		August 15, 2007	2.0 MB

Using DirectDraw as replacement for OpenGL

3. If this still does not help, Delta2D can use on Microsoft Windows 2000, XP and Vista DirectX instead of OpenGL for 3D-representation. It does not look as nice as with OpenGL, but it can be helpful though. Please follow these steps:
   
   Quit Delta2D.

   For Delta2D 4.0 and newer

   • Locate the folder of your Delta2D-installation, mostly something like "C:\Program Files\DECODON\Delta2D"
   • In the subfolder etc you can find the file called "Delta2D.conf"; open it with any editor.
   • Please append

     -J-Dj3d.rend=d3d

     at the bottom so that it looks like that:

     default_options="-J-Xms32m -J-Xmx2048M -J-XX:PermSize=32m -J-XX:MaxPermSize=128m -J-XX:+UseConcMarkSweepGC 
     -J-XX:+CMSClassUnloadingEnabled -J-Dswing.disablevistaanimation=true -J-Dsun.java2d.d3d=false -Dj3d.rend=d3d"

   • Save the file.

   For Delta2D 3.5 and 3.6

   • Locate the folder of your Delta2D-installation, mostly something like "C:\Program Files\DECODON\Delta2D\3.5"
   • Open the file called "Delta2D.vmoptions" with any editor.
   • Please append

     -Dj3d.rend=d3d

     at the bottom so that it looks like that:

     -Xmx512M
     -Xms64M
     -Xverify:none
     -Dj3d.rend=d3d

   • Save the file.

   For Delta2D 3.4 and earlier

   • Locate the folder of your Delta2D-installation, mostly something like "C:\Program Files\DECODON\Delta2D\3.4"
   • Open the file called "Delta2D.lax" with any editor and find the line reading
     
     lax.nl.java.option.additional=-Xmx512M -Xverify:none -XX:MaxGCPauseMillis=5000 -XX:GCTimeRatio=9
     
     (Please note that the values for -Xmx can vary, so do not do a literal search for the complete line)
   • Please add

     -Dj3d.rend=d3d

     to the line so that it looks like that:
     
     lax.nl.java.option.additional=-Xmx512M -Xverify:none -XX:MaxGCPauseMillis=5000 -XX:GCTimeRatio=9 -Dj3d.rend=d3d
     
     
   • Save the file.
   
   Start Delta2D.


4. Reset the virtual memory settings in your Windows Settings to system managed size. Reboot your computer if necessary.