This chapter shows how to set up and configure user accounts for QUANTA.
To start the program, type the following line at the shell prompt:
Now you have an alias named quanta. To run a one-time test of the installation, type the alias name as the command to run the program:
The .cshrc file of each user authorized to run QUANTA must source the installed .setquanta file. Edit the .cshrc file of each qualified user, adding the following line:
source ~accelrys/quanta97/.setquanta
After the next login, you can type this command to invoke the program:
To install database.dat in an exising QUANTA installation do the following:
1. Make sure your QUANTA environment is initialized.
2. Change to the directory containing this README:
3. Backup your existing database.dat file:
4. Copy the database.dat file in this directory to your QUANTA installation directory:
SGI boxes must be configured to run in 24 bit TrueColor mode to run the X11 version of quanta.
True Color mode is an X windowing environment mode on IRIX that enables applications to make use of the 24-bit color depths available on video cards and monitors. This color depth is supported by all SGI workstations Octane and newer. Graphics intensive programs typically require True Color.
2. As a precaution before editing, make a backup copy of the file /var/X11/xdm/Xservers.
3. Edit /var/X11/xdm/Xservers as follows:
Original: :0 secure /usr/bin/X11/X -bs -nobitscale -c -pseudomap 4sight -solidroot sgilightblue -cursorFG red -cursorBG white
Change to: :0 secure /usr/bin/X11/X -bs -nobitscale -c -class TrueColor -depth 24 -solidroot sgilightblue -cursorFG red -cursorBG white
4. Run the following command (logging out does not reset the display):
(/usr/gfx/stopgfx; /usr/gfx/startgfx)&
Running QUANTA in stereo in a window mode on SGI requires that you have pre-configured your X Server to support hardware stereo. This configuration is typically performed by the root user using the /usr/bin/X11/xsetmon command. xsetmon provides an interactive interface to select the video mode as the default value for future X Windows sessions. Changing video modes typically requires restarting the X Server, which is accomplished by logging out and logging back in.
When selecting a mode for QUANTA stereo, be aware that only modes ending in "s" support hardware stereo. Also note that refresh rates around 100Hz or better produce the most realistic stereo image in the application (since each eye is refreshed at 50Hz). For example, on the workstations at Accelrys we typically use the 1280x1024_96s mode, which gives a resolution of 1280x1024 pixels and a refresh rate of 96Hz.
For more information on using xsetmon and video modes please refer to the SGI IRIX system administration guides. You can also access the xsetmon and related manual pages from the SGI website:
To test these changes from within QUANTA, perform the following steps:
3. To view molecules in stereo, select View | Stereo | Stereo in a Window or type VIEW SWIN.
Running QUANTA in Stereo in a Window mode on Linux requires that you have configured your XF86Config file set to enable the "Stereo" option. Once you have downloaded and installed the NVidia drivers, you must make changes to the file /etc/X11/XF86Config-4 as follows:
1. Make sure the "Device" section is using the "nvidia" driver.
2. Add the following line to the "Screen" section:
Option "Stereo" "3"
Examples of these sections are below:
Section "Device"Identifier "Device0"
Driver "nvidia"
VendorName "Device0"
BoardName "Device0"
EndSection
Section "Screen"
Identifier "Screen0"
Device "Device0"
Monitor "Monitor0"
DefaultDepth 24
Option "Stereo" "3"
Subsection "Display"
Depth 24
Modes "1600x1200"
EndSubsection
EndSection
To test these changes from within QUANTA, perform the following steps:
3. To view molecules in stereo, select View | Stereo | Stereo in a Window or type VIEW SWIN.