Web: Installation on Linux

• 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 with Motif Widgets. JWeb written in Java is also available for installation on GNU/Linux but lacks much functionality present in Web.

• Web INSTALLATION

  1. Download and uncompress the Web distribution and place it in an appropriate directory: PARENT-DIR.

     The following Web directories will be created under: PARENT-DIR:

     Directory	Contents
     web/src	Web Source code, libraries
     web/bin	Web Executables
     web/docs	Web Documentation
     web/xlibs	Web Sample Motif object libraries
     web/jweb	JWeb directory

     The PARENT-DIR/web/bin directory contains following GNU/Linux executable binary files, use whichever one works best on your system.

     Web	For Desktop Environment	Visual	Executable	Library linkage
     web_linux_dir	KDE and most others	24 bit DirectColor	32 bits	Dynamic
     web_linux_dirs	KDE and most others	24 bit DirectColor	32 bits	Static
     web_linux_tru	Gnome	24 bit TrueColor	32 bits	Dynamic
     web_linux_trus	Gnome	24 bit TrueColor	32 bits	Static
     web_linux_trud64	KDE/Gnome/Etc	24 bit TrueColor	64 bits	Dynamic

  2. Set "web"Command using one of these options:

     1. 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_dir
        or
        alias web PARENT-DIR/web/bin/web_linux_tru
        

     2. Place the web executable(s) in: /usr/local/bin which is probably already in your search PATH.
     
     
     3. Modify your search path to include the PARENT-DIR/web/bin directory.

• 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
  

• If Web does not run

  • If you get an error 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 ...:

    Your system may not have the standard run-time X Window libraries.
    Web executables: web_linux_trus and web_linux_dirs have been statically linked with X and Motif libraries and should not have a problem with missing libraries.
    However the other Web executables require the following X Window libraries: libXt.so.6, libX11.so.6, libm.so.6, libSM.so.6, libICE.so.6, libxcb.so.1, and libXau.so.6.
    d And the following Motif libraries: libXmu.so, and libXp.so
    
    If web_linux_trus or web_linux_dirs does not preform satisfactorily on your sytem you will have to install X Window and Motif libraries.

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

    Perhaps Web can not find the location of the standard run-time X Window libraries.

    On Redhat and SUSE Linux for 32 bit applications these libraries are often in: /usr/X11R6/lib (or more recently in: /usr/lib/). If your system does not know the location of your X Window libraries and 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

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

    You have a bad X Window - Visual selection.
    A possible reason for this message is that you have an Nvidia graphics card and are trying to use the default open source graphics driver that came with your Linux distribution. Download the appropriate FREE driver from Nvidia and you will get better graphics for both SPIDER and other programs. If you still get this error message after restarting your graphics system then your graphics card fails to support the necessary visual or your X-Window installation has limited your machines visual support. You may be able to use the alternative Web executable (see above table).

  • 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 24 bit, directcolor visual!
    XError of failed request: Bad Color (invalid colormap parameter).

    The usual reason for this message is that you have an Nvidia graphics card and are trying to use the default open source graphics driver that came with your Linux distribution. Download the appropriate FREE driver from Nvidia and you will get better graphics for both Web and other programs. If you still get this error message after restarting you graphics system then your graphics card fails to support the necessary visual or your X-Window installation has limited your machines visual support. You can use JWeb instead.

  • 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 24
    Provide a password if prompted.
    

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

    vncviewer :1
    Provide a password if prompted.
    

    Opens new desktop within a window
    Here you can start web_linux_dir 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 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 JWeb instead.

• If Web runs but has problems/bugs

  • If you are using Web-linux_dir and it 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-linux_dir 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 you dislike the color flashing you can use: Web-linux_tru instead.

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

    SUSE X11.0 X Window 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-linux_dir runs but the pulldown menus become invisible:

    • If you are using the KDE Window Manager, the Window Manager is installing its own color choices for Web menus and you must override this.
      For KDE 3.* access the setting under:

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

      For KDE 4.* access the setting under:

      'Personal Settings (Configure Desktop)'--
      'Appearance' or 'Application' --
      'Colors' or 'Color Settings' --
      'Options' --
      'Apply colors to non-KDE applications'
      And insure it is set: OFF

    • If you are using GNOME window manager and you still are having problems with invisible menus:

      You can try:

      Switch to KDE window manager,

      Use: web_linux_tru instead,

      Use: web_linux_trud64 instead.

  • If you are still unable to get Web to run properly or have suggestions, I do not know who to contact as I can't remember much about this software anymore.

  
  

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  Source: web-inst-linux.html     Updated: 3/16/25     ArDean Leith