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Options

The game includes full control customisation, accessible from the usual place in the menu. However, the default settings provided from the Quake pak files aren't too enjoyable when using them on the DS, so feel free to use my config file.
Don't forget that after making changes to the settings, you must use the 'SAVE SETTINGS' option to actually save your settings to disk. Quake would normally do this when you quit, but you don't really use the quit option on the DS! I may put in an auto-save option...

Current controls:
The config menu also contains DS specific options:
There are more options available in the config file:

Transparent water

Quake does not natively support transparent stuff due to the way the maps are built. However there have been patches to Quake to allow you to get transparent water (and sludge, teleporters, lava etc) over the years, and I've added support for this to QuakeDS.
Read here if you want details of the regular Quake way, as most of the details apply. http://retroquake.planetquake.gamespy.com/blog/?p=34
To summarise, there seem to be two ways to do it:
Once you've done this, to get Quake to render stuff with transparency, adjust the ds_turb_transparency variable in the range of 0-30. Zero means invisible water, 30 means pretty much opaque. If you set it to 31 you'll disable transparency all together - this is the default.