Web: Installation on Linux

Contents

1. GENERAL
2. LOADING
3. INSTALLATION
4. COMPILATION, LINKING, & LIBRARIES
5. TESTING
6. RUNNING
7. BUGS

1. GENERAL

   Web is a point-and-click interface for display and interaction with SPIDER images and data. Web is written in C for use with the X WINDOW system under Motif. JWeb written in Java is also available for installation on GNU/Linux but still lacks some of the functionality present in Web.

2. LOADING THE SPIDER/WEB DISTRIBUTION
   (May have already been done if you have installed SPIDER!)

   1. Download SPIDER/Web and place it in an appropriate directory: PARENT-DIR.
      The compressed SPIDER/Web distribution takes about 220 Mb of disk space. The uncompressed whole distribution will take about 850Mb but includes libraries and executables for many different systems some of which can be discarded.
   2. Uncompress the distribution file e.g.
      gunzip spiderweb.tar.gz
   3. Unpack the tar archive e.g.
      tar -xvf spiderweb.tar*

   The following Web directories will be created under: PARENT-DIR (along with other directories for SPIDER, etc.):

   Directory	Contents
   web/src	Web source code, libraries
   web/bin	Web executables
   web/docs	Web documentation, html pages
   web/rgb	rgb color look-up-tables
   web/AppPlusS	AppPlusS widget for Linux 32 bit OS
   web/AppPlusS_osx	AppPlusS widget for OSX on PPC
   web/java	JWeb directory

3. INSTALLATION

   The PARENT-DIR/web/bin directory contains following GNU/Linux executable binary files:

   Web	Optimal byte-ordering	Visual	Notes
   web_linux_24	SGI	24 bit DirectColor	Try this exectable first
   web_linux	SGI	8 bit PseudoColor	Refer to: Using 8 bit Web

   1. Set "web" Command

      You can define an alias for your Web location. Assuming you are using the 'C' shell, you would put a line similar to the following in the .cshrc startup file in your home directory:

      alias web PARENT-DIR/web/bin/web_linux_24
      

      If you do not have a .cshrc file in your home directory you can create it with any text editor.
      Alternatively, you could place the web executable in: /usr/local/bin which is probably already on your search PATH or you could modify your search path to include the PARENT-DIR/web/bin directory.

   2. Set environment variables.

      You also need to tell Web the location of your *.rgb color-look-up-table files and manual pages. If you are using the 'C' shell, place following lines in your .cshrc startup file:

      setenv SPRGB_DIR "PARENT-DIR/web/rgb"
      setenv WEBMAN_DIR "PARENT-DIR/web/docs"

   3. Set location of run-time libraries.

      You may need to tell Web the location of the shared run-time X Window and Motif libraries. On Redhat and SUSE Linux these libraries are often in: /usr/X11R6/lib. If you are using the 'C' shell add the following lines to your .cshrc startup file

      if ( $?LD_LIBRARY_PATH ) then

          setenv LD_LIBRARY_PATH $LD_LIBRARY_PATH:/usr/X11R6/lib

      else

          setenv LD_LIBRARY_PATH /usr/X11R6/lib

      endif

   4. Set X window resources.

      Place contents of: PARENT-DIR/web/src/Web_resources_linux24 in your X window resource startup file. Typically this is: .Xdefaults in your home directory. After altering .Xdefaults you may have to restart your window manager by logging in again. (This depends on how resources are set on your system.) If you do not have a .Xdefaults in your home directory you can create it with any text editor.

4. Testing Web.

   Use your web command to start Web.

   If Web does not run

   • If you get an error message like: Command not found

     See "Set Web command" above to ensure that your desired executable is accessible.

   • If you get an error message about a Missing library ...:

     On some distributions the Motif libraries are not istalled with the default installation. If not, you will have to install the following Motif libraries from your Linux distribution: libXm, and libXmu. The following X Window libraries which are usually installed by default from your distribution are also necessary: libXt, libX11, libXau, libXdmcp, and libXext.

   • If you get an X Window error message like: Bad Match ....

     You have a bad X Window - Visual selection.
     Be sure you have set Web X window resources" as described above. If it still does not work try logging out and logging in again. If it still gives that message try executing xrdb -load ~/.Xdefaults in the terminal window before you start Web.

   • If you get an message listing the Screen depth as 16 bits followed by an error message like: XError of failed request: Bad Value ......

     You need to change the number of colors displayed by your graphics card from: 16 bits to: 24 bits.
     E.g. if you are using SUSE
     

     'Start up YAST' --
     'Under: Hardware' --
     'Under: Graphics Card & Monitor' --
     'Change colors to (24 bit)'
     You may have to login as root to do this.

   • If you get an error message like: No 24bit, directcolor visual!
     XError of failed request: Bad Color (invalid colormap parameter).

     Either your graphics card fails to support the necessary visual or your X-Window installation has limited your machines visual support. You can use 8 bit Web or JWeb instead.

   • If Web still does not run:

     Try compiling and linking Web on your system. This is usually easy if you have already installed the necessary X-window and Motif development headers and libraries on your system

   • If Web still fails to run:

     Use vnc (Virtual Network Computing) to create a virtual display.

     Most GNU/Linux distributions include vnc in their default installation which can be used to create a virtual display in a window on your current desktop.
     When vnc is installed:

     vncserver -cc 3 -depth 8
     Provide a password if prompted.
     

     Returns "New 'X' desktop is hostname:number"
     e.g.: "New 'X' desktop is green:1"
     

     vcnviewer :1
     Provide a password if prompted.
     

     Opens new desktop within a window
     Here you can start web_linux (use web_linux.* NOT: web_linux_24.8) normally or you can start it automatically by editing your vnc viewer startup file: ~/.vnc/xstartup

     vncserver -kill :1
     Kills the vnc server. (The vnc server will usually keep the same passwords you specified for the next invocation.)
     

   • If Web still fails to run:

     Use JWeb instead.

   If Web runs and but the other windows on the screen have strange colors when the Web window is in use (has focus).

   • This is expected.

     Web installs its own colormap so that it can use private colormaps for intensity display. This is an old (and powerfull) technique for visualization which is disappearing these days but still exists in Web.

   If Web runs and but the pulldown menus have boxes instead of letters on SUSE 11.0

   • SUSE X11.0 XWindow fonts are broken.

     Update to SUSE 11.1 or just update following packages.

     xorg-x11-fonts-core
     xorg-x11
     xorg-x11-fonts
     xorg-x11-server

   If Web runs and but the pulldown menus become invisible

   • If you are using the KDE Window Manager:

     Your Window Manager may be installing its own color choices for Web menus and you must override this.
     Access the setting under:
     

     'Control center' --
     'Appearance & Themes' --
     'Colors' --
     'Apply colors to non-KDE applications'
     And insure it is set: OFF

   • If you are using GNOME window manager or the problem persists with KDE:

     Some of the X Window settings from your .Xdefaults file (and elsewhere) may be interfering with the values necessary for using Web. You can override these settings by issuing the following command in the terminal window where you intend to start Web:
     xrdb -load PARENT-DIR/web/src/Web_resources_linux24
     This will have to be done each time you want to start Web so maybe you should create a small script to do it.

   • If you are using GNOME window manager and you still are having problems with invisible menus after making the above changes

     You can switch to KDE, use VNC, or use JWeb instead.

   If you are still unable to get Web to run properly contact us at the address below. Please send complete info on what you are trying to do, exact error messages, Linux distribution type, platform (AMD or Intel,etc), Window Manager in use (KDE, GNOME, etc.), the value of environment variable: LD_LIBRARY_PATH, and output from: xrdb -query command.

5. Using Web

   To control Web: USE MOUSE TO SELECT MENU ITEMS FROM PULL-DOWN MENUS

   Further information is given in the Web manual.

   You may enter the file extension on the command line, e.g.:

   web dat
   

6. BUGS & SUGGESTIONS

   In the event that you have questions about methodologies or wish to report bugs please send us complete info on what you are trying to do, including any error messages.

   Send this info to:

   ArDean Leith
   phone: 518-486-5604
   email: spider@wadsworth.org
   www: www.wadsworth.org/spider_doc/web/docs/web.html