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 some functionality present in Web.

• Web INSTALLATION

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

     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/jweb	JWeb directory

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

     Web	For Desktop Environment	Visual	Executable	Optimal byte-ordering
     web_linux_dir	KDE and most others	24 bit DirectColor	32 bits	Big-endian
     web_linux_tru	Gnome	24 bit TrueColor	32 bits	Big-endian

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

     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.

  3. Set environment variables.

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

     setenv SPRGB_DIR "PARENT-DIR/web/rgb"
     

• 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 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 ...:

    Your system may not have the standard 32 bit run-time X Window libraries. Web requires the following standard X Window 32 bit libraries: libXt.so.6, libX11.so.6, libm.so.6, libSM.so.6, libICE.so.6, libxcb.so.1, and libXau.so.6. (Web has been statically linked with the Motif libraries and no longer requires that you install Motif libraries).
    If you have a 64 bit OS and have not installed the 32 bit X Window libraries you will need to do so to use the precompiled executables For distributions which use apt-get this can be done:

    sudo apt-get install libxmu6:i386

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

    Your system 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) or use JWeb instead.

  • 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).

    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 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-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:

      Switch to KDE window manager,

      Use: web_linux_tru, or

      Use: JWeb instead.

  • If you are still unable to get Web to run properly or have suggestions, Please contact us and enclose the following info:

    What you are trying to do, exact error messages (if any), Linux distribution type, platform (AMD or Intel,etc), Window Manager in use (KDE, GNOME, etc.), the value of environment variable: LD_LIBRARY_PATH, and the output from: xrdb -query system command.

    ArDean Leith
    Phone: 518-486-5604
    Email: spider@wadsworth.org
    

  
  

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  Source: web-inst-linux.html     Updated: 05/05/13     ArDean Leith