Please check the symptoms and suggestions below, to see if that fixes the problem. If that does not help, email us at: npcml@scarletline.com. Try to include information about the browser and operating system that you are using, and a link to a page that demonstrates the problem.
Most Windows Vista specific problems are caused by UAC. Please try disabling UAC and see if it fixes the problem.
Disable UAC
If you see a black rectangle with "Loading ..." written in it, and it is not replaced within a couple of seconds, then the molecule file which has been embedded is probably unavailable. Usually this is caused by:
- If you are using Windows Vista, then this is probably a UAC configuration error. See your administrator or use a different OS.
- the web server having insufficient privileges to read the file
- a mis-spelled file name
- file name containing wrong-case characters
Please check with the web site administrator.
If you are using Windows Vista, then this is usually caused by an over-zealous Windows Vista UAC error. See your administrator or use a different OS. Otherwise, the file may be in an older incompatible variant of CML.
The file was not recognized as the reported MIME type. This happens when the molecular data file does not conform to the stated MIME type. This can be caused by:
- setting the wrong MIME type in the object or embed tag
- errors in the file itself, or
- a file written to an older and incompatible specification from the current
standard. Please check with the web site administrator.
All molecular types are internally converted to CML before being displayed. With extremely large and complex molecules, this conversion can take a minute or more. This delay can be removed entirely by providing the molecule already in CML format on the web page. If you wish to convert a molecule to CML format, simply right-click -> View CML Source on the molecular view. Then you can highlight all, cut and paste to a text editor, and save as ....
If you have multiple large macromolecules all animated or spinning on a browser page, this may result in sluggish performance of the browser. I suggest that you switch off spinning and animation in all but one or two macromolecules at a time.
On some machines, the OpenGL shadow rendering can cause artifacts such as black horizontal lines if the default sample size is not large enough. This can usually be fixed by installing the latest OpenGL drivers on your computer. You may also wish to consider upgrading the graphics capability of your workstation as this will give many visual improvements for little cost.
On some machines, the OpenGL default depth buffer quantization is too small. The result is that objects will pass in front of other closer objects. This can usually be fixed by installing the latest OpenGL drivers on your computer. You may also wish to consider upgrading the graphics capability of your workstation as this will give many visual improvements for little cost.
Either OpenGL is not installed on your computer, or it is not sufficiently powerful enough to render 3D molecules. This can usually be fixed by installing the latest OpenGL drivers on your computer. You may also wish to consider upgrading the graphics capability of your workstation as this will give many visual improvements for little cost.
This is a known bug in Firefox v3.x and SeaMonkey v2.x
Bugzilla Bug 505135
This is now fixed, please uninstall and re-install from a new download of the plugin.
Many browsers need to be completely stopped ( Quit on Mac OS X ) and restarted before they will recognize a newly installed plugin.
In some circumstances, earlier versions of Safari do not load the plugin (v2.0.4), and I suggest upgrading to a more recent version
You may have a missing dependency. To check this, please download and run the following file. You may have to right-click -> save link as if your mime types do not support shell scripts. The file should end up as check_npcml.sh in your home directory ( i.e. ~/check_npcml.sh ) and should have execute permission ( i.e. chmod 777 ~/check_npcml.sh )
check_npcml.sh
To use it, do the following:
1) Open a terminal window
2) Check that the file has execute priviledge, e.g.:
chmod 777 ./check_npcml.sh
3) Run the file:
./check_npcml.sh
4) Email the resulting check_npcml.txt file to npcml@scarletline.com
5) If you see any <name> => not found messages please find and install the relevant libraries, as follows
Missing libraries can be found and installed as follows:
- Debian based systems, such as Ubuntu:sudo apt-cache search <library-name>
- Mandriva:sudo urpmf <library-name>
- Fedora:sudo yum search <library-name>
and then, to install the package:
- On Debian based systems, such as Ubuntu:sudo apt-get install <package-name>
- On Mandriva:sudo urpmi <package-name>
- On Fedora:sudo yum install <package-name>
Thank you to Konstantin Tokarev for improvements to this section.
Try turning off "Enable 3D Acceleration" to avoid bugs in the OpenGL driver layer. This only seems to affect VirtualBox v3.X, earlier versions do not seem to have these bugs.
