Web: Installation on Mac OSX

Contents

1. GENERAL
2. LOADING
3. INSTALLATION
4. TESTING
5. RUNNING
6. 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. Thanks to Dr. Ngai Shing Mogk and Dr. Neil Ranson from the University of Leeds for porting Web for use on OSX. NOTE: We have reports that the Leopard Release of OSX 5.0 is buggy when used with X-Windows applications.

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 180 Mb of disk space. The uncompressed whole distribution will take about 850Mb but includes libraries and executables for several 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/src/osg	OpenMotif source code, misc. Mac files
   web/bin	Web executables
   web/docs	Web documentation
   web/rgb	Color look-up-tables
   web/java	JWeb directory

3. INSTALLATION

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

   Web	Platform	Visual	Libraries	Startup file	Makefile
   web_OSX_intel	Intel	8 bit	Static OpenMotif	web8-osx.zsh	Makefile_osx_intel
   web_OSX_intel_dy	Intel	8 bit	Dynamic OpenMotif	web8-osx.zsh	Makefile_osx_intel
   web_osx_ppc	PPC	8 bit	Dynamic Motif	-	Makefile_osx_ppc

   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/web8-osx.zsh
      

      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 (PARENT-DIR/web/bin/web8-osx.zsh) 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.

      NOTE:
      In order to use Web's 8 bit visual without interfering with use of other applications which need a 24 bit visual use the script: PARENT-DIR/web/bin/web8-osx.zsh This script will allow you to have multiple instances of the display manager running at different colour depths. The Mac's screen depth can still set to 'millions' of colours in the X11 preferences panel. Web is started by typing "web $datacode", creating a new instance of an 8bit display. This allows 24 bit software to coexist on the same physical display as Web, without any annoying colour glitches as the mouse moves from one to the other. See explanation at: .

   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 will need to tell Web the location of shared run-time X Window and Motif libraries. XWindow libraries may in: /usr/X11R6/lib. If you are using the OSX Motif run time libraries from Web they are located in: PARENT-DIR/web/osx/openmotif/lib
      . If you are using the 'C' shell add the following lines to your .cshrc startup file

      if ( $?DYLD_LIBRARY_PATH ) then

          setenv DYLD_LIBRARY_PATH $DYLD_LIBRARY_PATH:/usr/X11R6/lib:PARENT-DIR/web/osx/openmotif/lib

      else

          setenv DYLD_LIBRARY_PATH /usr/X11R6/lib:PARENT-DIR/web/osx/openmotif/lib

      endif

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 ...:

     Ensure that the following run time libraries are installed from your distribution: libXm, libXt, libX11, libXmu, libXau, libXdmcp, libfreetype and libXext. Also if you are using dynamic Motif libraries make sure that your DYLD_LIBRARY_PATH includes: PARENT-DIR/web/osx/openmotif/lib

   • 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 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 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 (PPC or Intel), the value of environment variable: DYLD_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