XtalView 2.0 Available from SDSC

Lynn F. Ten Eyck teneyckl at sdsc.edu
Wed Feb 9 18:04:48 EST 1994


*************************************************************************
*                                                                       *
*      The Computational Center for Macromolecular Structure (CCMS)     *
*                                                                       *
*************************************************************************
*                                                                       *
*                                                                       *
*                             X t a l V i e w                           *
*                                                                       *
*                               release 2.0                             *
*                                                                       *
*                                                                       *
*        (C) The Scripps Research Institute and Duncan E. McRee         *
*                       10666 N. Torrey Pines Rd.                       *
*                          La Jolla, CA 92037                           *
*                                                                       *
*                                                                       *
*     Author:         Duncan E. McRee, TSRI                             *
*     Contributors:   Alex Shah, Andy Arvai, and Mike Pique             *
*                                                                       *
*                                                                       *
*  README revision date February 8, 1994                                *
*                                                                       *
*  This file contains general information and installation              *
*  instructions.                                                        *
*                                                                       *
*                                                                       *
*************************************************************************


XtalView is a complete package for solving a macromolecular crystal
structure by isomorphous replacement, including building the
molecular model.  It runs on Sun, DEC, and SGI computers and takes
full advantage of the modern workstation environment.  It has a
simple but comprehensive windows based interface.  XtalView
maintains log files of the computations done.  Standard file
formats are used, which facilitates communication between XtalView
and programs such as X-PLOR, TNT, and MERLOT.

XtalView is described in the book 'Practical Protein
Crystallography' by Duncan McRee, who also designed the program.

XtalView is free for non-profit use.  For-profit users should
contact Duncan McRee (dem at scripps.edu) concerning licensing.  A binary
distribution is available through CCMS' e-mail responder; source code
is also available, but requires a signed license.

To receive information on obtaining XtalView software, send e-mail to:

    ccms-request at sdsc.edu

    leave the SUBJECT  line blank

    type ' get xtalview ' in the message


#####################

SUPPORT:

#####################

email:        ccms-help at sdsc.edu

telephone:    (619)534-5100

#####################

INSTRUCTIONS:

#####################

You must do three things before you can use XtalView:  

  Install the distribution
  Set up the XtalView environment
  Build the programs

Please see the DISK USAGE section below for information on the size of
the distribution.

Please see the README file in the src directory for notes on 
recompiling the programs

IMPORTANT--IF YOU USE IRIX 5.x OR SunOS 5.x SEE THE NOTE AT THE
           BOTTOM OF THE INSTRUCTIONS SECTION

#####

INSTALLING THE DISTRIBUTION:


XtalView is distributed in three parts.  The file xtalview.tar.Z contains
the platform independent parts of the distribution, while the files
xtalview_sun4SunOS4.tar.Z, xtalview_decmipsULTRIX4.tar.Z, and
xtalview_sgi4dIRIX4.tar.Z contain the platform dependent files for each
supported hardware/software platform.  The file xtalview_src.tar.Z
contains the source to XtalView and requires a separate license. 


* Create a separate directory for XtalView, and change to the newly 
  created directory.

     mkdir XtalView 
     cd XtalView

* Download xtalview.tar.Z and the platform dependent file(s) for the
  platform(s) on which you are installing XtalView (i.e.,
  xtalview_sun4SunOS4.tar.Z, xtalview_decmipsULTRIX4.tar.Z, or
  xtalview_sgi4dIRIX4.tar.Z).  Make sure that these files are in your
  XtalView directory, and that you have downloaded at least two files.

* If you installing the XtalView source, also download
  xtalview_src.tar.Z.

* Uncompress and unpack the archived files.  Make sure you do 
  xtalview.tar.Z first:

     uncompress -c xtalview.tar.Z | tar xvpf -

  Now uncompress and unpack the archived file specific for your platform:

     uncompress -c xtalview_sun4SunOS4.tar.Z  | tar xvpf -
                          OR
     uncompress -c xtalview_decmipsULTRIX4.tar.Z | tar xvpf -
                          OR
     uncompress -c xtalview_sgi4dIRIX4.tar.Z | tar xvpf -

  Finally, if you are installing source, uncompress and unpack the
  source archive:

     uncompress -c xtalview_src.tar.Z | tar xvpf -

  IMPORTANT--Make sure you use the "p" option to tar in the above
             commands.  Note, however, that some DECstations may give
             a warning that the "p" option will only affect files that
             you own.  You can safely ignore this warning.

* You may now delete the *.tar.Z files.

     NOTE--At this point, you will not be able to find most of the
           XtalView binaries.  Don't be alarmed.  Because the
           XtalView binaries are both numerous and large, most of
           them have not been included in the distribution. You
           must build them from object code once the distribution
           has been installed.  See the "Building the Programs"
           secion below.

#####

SETTING UP THE XTALVIEW ENVIRONMENT

     NOTE--Silicon Graphics users should read the file
           $XTALVIEWHOME/make_sgi4dIRIX4/README 
           for additional instructions.

* Copy the XtalView.env file to your home directory.  This file is
  located in the top directory of the XtalView distribution.

* Edit the XtalView.env file.  You must edit three lines:

    Set the XTALVIEWHOME environment variable to the location of the
    XtalView distribution; i.e., the directory you created in the first
    step of installing the distribution.  Make sure you use the full
    path name to the directory.

    Set the CRYSTALDATA environment variable to the directory where your
    crystal data is (or will be)located.  Again, make sure you use the
    full path name.  If this directory does not already exist, you must
    create it before you can use XtalView

    Set the CRYSTAL environment variable to the name of your default 
    crystal

* The commands in the XtalView.env file must be executed before you can
  use XtalView.  To do this, put the line

    source ~/XtalView.env

  in your .cshrc file.

* XtalView requires fonts that may not be installed on non-Sun machines.
  These fonts are included in the XtalView distribution (in the directory
  $XTALVIEWHOME/fonts), but the procedure to install them depends on how
  you will be running XtalView.

1) You are running XtalView locally (i.e., NOT over a network):

     Execute the command $XTALVIEWHOME/bin/share/fonts.  You only need
     to do this once each time you log in to your workstation.
     NOTE: the  XtalView.env file must have been sourced before this
     will work.

2) You are running XtalView remotely: 

  a) The machine independent part of the XtalView distribution is
     available on your local workstation.

     BEFORE you log on to the remote machine, Execute the command
     $XTALVIEWHOME/bin/share/fonts.  You only need to do this once each
     time you log in to the local workstation.  NOTE: the 
     XtalView.env file must have been sourced before this will work.

  b) The machine independent part of the XtalView distribution is NOT
     available on your local workstation.

     i) your local machine is a UNIX workstation

        Copy the $XTALVIEWHOME/fonts directory and the script 
        $XTALVIEWHOME/bin/share/fonts to the local machine.  Set the 
        XBIN and XTALVIEWFONTSDIR variables in the fonts script to the 
        directories that hold the standard X binaries (e.g. /usr/bin/X11)
        and the XtalView fonts, respectively.  Execute the fonts script.
        You only need to execute the edited script once each time you log
        in to the local workstation.

    ii) Your local machine is not a UNIX workstation (e.g., its an X
        terminal)

        Consult your system's documentation for information on setting up
        the font path.  Besides adding the $XTALVIEWHOME/fonts directories
        to the font path, you must also move any 100dpi directories to the
        end of the font path.

#####

BUILDING THE XTALVIEW PROGRAMS

Because the XtalView package contains a large number of programs, 
to save disk space, binaries are not included in the distribution.
To build the binaries, move to the $XTALVIEWHOME directory and type

    make all

to load all the programs, or

    make program-name

to load a specific program. 

This process must be repeated on each hardware/software platform on which
you have installed XtalView.  

     NOTE--On Sun workstations, xfit will not work unless
           the XGL run-time environment has been installed. 
           This software is bundled with the operating system.

     NOTE--The xfit binary _IS_ included in the Sun version
           of the XtalView distribution.

The XtalView package is now ready for use.  The programs can be started
individually or through the xtalmgr program.  On some systems, you may
receive a message similar to:

    System warning: No such file or directory, extras menu file
    /usr/lib/.text_extras_menu (Textsw package)

You can disregard this message or suppress it by becoming superuser and
entering the command:

    touch  /usr/lib/.text_extras_menu


NOTE FOR USERS OF IRIX 5.x OR SUNOX 5.x:

Currently, XtalView can run, but cannot be compiled or loaded under these
operating systems.  If you have access to a machine running IRIX 4.x
or SunOS 4.x, install the distribution on this machine as outlined
above.  Next, download xtalview_sgi4dIRIX5.tar.Z and/or
xtalview_sun4SunOS5.tar.Z and unpack it as above.  This will allow you
to use the 4.x binaries on the 5.x machine.

If you do not have access to a machine running IRIX 4.x or SunOS 4.x,
follow the above steps, but do not issue the 'make all' command.
Contact CCMS (see SUPPORT section above), and we will provide you with
the XtalView binaries.


#####################

DISK USAGE

#####################

The compressed and uncompressed sizes of the distribution files (in MByte)
are as follows:

    FILE                                COMPRESSED       UNCOMPRESSED 

    xtalview.tar.Z                      2.21             6.88
    xtalview_src.tar.Z                  2.04             6.00
    xtalview_decmipsULTRIX4.tar.Z       4.45             9.78
    xtalview_sgi4dIRIX4.tar.Z           3.23             6.68
    xtalview_sun4SunOS4.tar.Z           4.52             9.54

Additional space is needed for the binaries, which are not included in
the 
distribution files (see the installation instructions above).  The disk
usage for the binaries is as follows:

    ARCHITECTURE          MBytes

    decmipsULTRIX4        52.27
    sgi4dIRIX4            49.67
    sun4SunOS4             7.11

XtalView does not employ shared libraries On decmips and sgi4d machines. 
On these systems, the binaries for the window-based programs are
approximately 2-3 MByte each. You can conserve considerable space by
building only the binaries that you need.

#####################

DOCUMENTATION

#####################

A postscript version of the XtalView User's Guide is in the doc
directory.  This file may be printed on a postscript printer or viewed
online with a postscript previewer such as ghostscript, pageview (Sun4),
dxpsview (decmips), or xpsview (sgi4d).  We recommend that new users
read the introductory sections of this manual.

Man pages for the XtalView programs are located in the man directory. 
The nroff source files are in the man1 subdirectory and the formatted
ASCII versions are in the cat1 subdirectory.  These man pages may be
incorporated into your site's man system, or you may print or view the
formatted versions directly using commands such as:

     lpr $XTALVIEWHOME/man/cat1/_name_.1

        or

     more $XTALVIEWHOME/man/cat1/_name_.1

where _name_ is the name of the man page.

#######################

DEPENDENCE ON SOFTWARE NOT DISTRIBUTED BY CCMS

#######################

* On Sun platforms, xfit requires that the xgl runtime environment be
  installed on your system.

* xskel requires that mkskel (part of the GRINCH package, available
  from the Department of Computer Science, University of North Carolina)
  be installed on your system.




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