Chimera on Mac OS X using X windows

Chimera for Mac OS X is available in X windows and native Aqua versions. With Chimera 1.4, we now recommend the Aqua version because most of problems with the current port of the Aqua Tk windowing toolkit have been resolved.

Contents

• Requirements
  • Installing X11 on Mac OS X 10.4
  • Installing X11 on Mac OS X 10.5
  • Installing X11 on Mac OS X 10.6
• Possible Problems Downloading Chimera
• Installation
• Removal
• Starting Chimera
• Known Problems with the X windows Version of Chimera

Chimera runs on Mac OS X 10.4 (Tiger), 10.5 (Leopard), and 10.6 (Snow Leopard), but not on older versions of Mac OS X.

A X11 server must be installed for Chimera to start. For 10.4, we recommend Apple's X server (X11). It is reliable and provides hardware OpenGL acceleration. For 10.5 and 10.6, we recommend getting a newer version of the X11 server from the XQuartz project because the graphics support is much better (although XQuartz won't support Mac OS X 10.6 until version 2.4.1 comes out).

X11 comes with Mac OS X as an optional component (standard location /Applications/Utilities/X11). See the Mac OS X 10.4, Mac OS X 10.5, or Mac OS X 10.6 instructions below.

1. insert the 10.4 installation disc,
2. double-click on Optional Installs.mpkg at the top level,
3. get to the Installation Type step,
4. expand the Applications section,
5. select X11, and
6. click Install.

Clicking to activate windows

Two X11 preference settings help avoid extra mouse clicks when using Chimera dialogs. When you move the mouse from one Chimera window to another you can automatically have the new window activated without requiring a mouse click. Set this "focus follows mouse" preference by typing the following command in a Mac Terminal window:

	  defaults write com.apple.x11 wm_ffm -bool true

The default behavior of the Quartz window manager from the Apple X server 1.0 release is to require you to click on each window before you can type to it or press buttons. The wm_ffm setting only effects X applications, not Aqua applications, so it only has an effect when an X window currently is active and you move the mouse to another X window.

When you are using a native Mac application (not X windows) and then click on a menu within the Chimera window the mouse click does not bring up the menu. It just activates the Chimera window and another mouse click is needed to show the menu. To make this work with a single mouse click, use the Mac X server wm_click_through preference by typing the following command in a Mac Terminal window:

	  defaults write com.apple.x11 wm_click_through -bool true

Normally Mac OS X swallows window-activating mouse events. This preference causes a window-activating mouse click on an X window to also be processed by the application.

Enabling hardware stereo in a window

Otherwise known as sequential stereo, is a rapid flickering between left-eye and right-eye views that produces a three-dimensional effect when viewed with special synchronized glasses. Sequential stereo in Chimera requires a workstation-class graphics card and a graphics driver configured for stereo. To tell X11 to make stereo visuals available, type the following command in a Mac Terminal window:

	  defaults write com.apple.x11 enable_stereo -bool true

X11 must be restarted after any of these settings are changed. The settings are saved in your ~/Library/Preferences directory, so they will apply to future sessions. Reissuing the commands with false instead of true will restore the default preference settings.

1. insert the 10.5 installation disc,
2. go into the Optional Installs folder
3. double-click on Optional Installs.mpkg
4. get to the Installation Type step,
5. expand the Applications section,
6. select X11, and
7. finish the installation procedure
8. do a software update to get the latest version

Note that if you have a one-button mouse, the X11 provided with 10.5 does not have three-button emulation on by default, which will make it impossible to translate and scale structures with the mouse. To turn on three-button emulation, do this:

1. click on the X11 icon (it should show up in the dock when you start Chimera)
2. open the X11 menu from the menubar at the top of the screen
3. choose the Preferences... entry
4. in the resulting dialog choose the Input tab
5. enable the Emulate three button mouse option

Clicking to activate windows

Two X11 preference settings help avoid extra mouse clicks when using Chimera dialogs. When you move the mouse from one Chimera window to another you can automatically have the new window activated without requiring a mouse click. Set this "focus follows mouse" preference by typing the following command in a Mac Terminal window:

	  defaults write org.x.X11 wm_ffm -bool true

The default behavior of the Quartz window manager from the Apple X server 1.0 release is to require you to click on each window before you can type to it or press buttons. The wm_ffm setting only effects X applications, not Aqua applications, so it only has an effect when an X window currently is active and you move the mouse to another X window.

When you are using a native Mac application (not X windows) and then click on a menu within the Chimera window the mouse click does not bring up the menu. It just activates the Chimera window and another mouse click is needed to show the menu. To make this work with a single mouse click, use the Mac X server wm_click_through preference by typing the following command in a Mac Terminal window:

	  defaults write org.x.X11 wm_click_through -bool true

Normally Mac OS X swallows window-activating mouse events. This preference causes a window-activating mouse click on an X window to also be processed by the application.

X11 must be restarted after any of these settings are changed. The settings are saved in your ~/Library/Preferences directory, so they will apply to future sessions. Reissuing the commands with false instead of true will restore the default preference settings.

Exposé

If some of your mouse buttons activate Exposé functions, you will likely want to use the Exposé category of System Preferences to make those buttons available for Chimera functions.

See the Mac OS X 10.5 instructions.

Automatically closing X11

Two X11 preference settings control the automatic closing of the X11 server. Turn it on by typing the following command in a Mac Terminal window:

	  defaults write org.x.X11 wm_auto_quit -bool true

And you control the timeout, in seconds, by typing the following command in a Mac Terminal window:

	  defaults write org.x.X11 wm_auto_quit_timeout -int 3

X11 must be restarted after any of these settings are changed. The settings are saved in your ~/Library/Preferences directory, so they will apply to future sessions. Reissuing the commands with false instead of true will restore the default preference settings.

If you experience difficulty downloading the distribution, try this link as a simple test to see if the size of the Chimera distribution is causing problems. The link should download a small Python program to your computer. The only difference between this and the Chimera distribution download is the size of the file, so if the link works then something in your environment is blocking the downloading of very large files.

If this test download does not work, then something in your environment is blocking the download of any binary file (the download is sent using the http content type of "application/octet-stream").

You can try downloading the Chimera distribution to a different computer or from a different network that you are sure does not make use of a proxy web server.

To install Chimera, open the disk image file you downloaded. This will put the Chimera application on your desktop. This may have happened automatically when you downloaded.

If more than one person will be using Chimera, the Applications folder is a good place to put it. Moving it to that folder requires administrator privileges. If it is only for your use, putting it in your home Applications folder or leaving it on the desktop are reasonable choices.

Removal

To remove Chimera, just drag it to the trash.

The usual method of starting Chimera is by double-clicking the icon. If you want to start it from the command-line (e.g., you want to run more than one chimera at a time), use the following executable:

	Chimera.app/Contents/MacOS/chimera

Removal Known Problems with the X windows Version of Chimera

• Display misconfiguration. Please increase the color quality ... You need to increase the color quality/depth. There are two places in Mac OS X that might be lowering the color quality. Normally the X11 application uses whatever you set your Display to. So first, bring the System Preferences, click on the Display icon in the Hardware category, then change the Colors value to Millions (instead of 256 Colors or Thousands). If it is set Millions and you're still getting this error, then you need to bring up the X11 application (see above), bring up its Preferences dialog, switch to the Output tab, and change Colors to Millions (or From Display if the system preference is Millions), and then quit the X11 application so the next time it starts, it has the additional color quality.

Laboratory Overview | Research | Outreach & Training | Available Resources | Visitors Center | Search