xtalview - a suite of programs for solving macromolecular
WHAT IS XTALVIEW
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 compu-
tations done. Standard file formats are used, which facili-
tates communication between XtalView and programs such as
X-PLOR, TNT, and MERLOT.
XtalView is described in the book 'Practical Protein Crys-
tallography' by Duncan McRee, who also designed the program.
XtalView is free for non-profit use. For-profit users
should contact Duncan McRee (email@example.com) 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
leave the SUBJECT line blank
type ' get xtalview ' in the message
For technical support, or any other questions, contact CCMS
SETTING UP THE XTALVIEW ENVIRONMENT
* Copy the XtalView.env file to your home directory.
This file is located in the top directory of the Xtal-
View distribution. Contact you system administrator if
you don't know where XtalView is installed.
* Edit the XtalView.env file. You must edit three lines:
1. Set the XTALVIEWHOME environment variable to the
location of the XtalView distribution. Make sure
you use the full path name to the directory.
2. 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 Xtal-
3. 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
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 make use of
them depends on how you will be running XtalView.
1) You are running XtalView locally (i.e., NOT over a
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
BEFORE you log on to the remote machine, Exe-
cute 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
b) The machine independent part of the XtalView
distribution is NOT available on your local
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 XTAL-
VIEWFONTSDIR 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
ii) Your local machine is not a UNIX worksta-
tion (e.g., its an X terminal)
Consult your system's documentation for
information on setting up the font path.
Besides adding the $XTALVIEWHOME/fonts direc-
tories to the font path, you must also move
any 100dpi directories to the end of the font
The XtalView package is now ready for use. You can access
the XtalView programs through the xtalmgr program, or you
can run them individually (see xtalmgr(1)).
Silicon Graphics users should read the file
$XTALVIEWHOME/make_sgi4dIRIX4/README for additional instruc-
A postscript version of the XtalView User's Guide is in the
$XTLVIEWHOME/doc directory. Each chapter is in a separate
file and may be printed on a postscript printer or viewed
online with a postscript previewer such as ghostscript,
pageview (Sun4), dxpsview (decmips), or xpsview (sgi4d).
The contents of the chapters are as follows. We recommend
that new users read the introductory sections of this
Chapter 1 (chapt1.ps)
Introduction provides an introduction to XtalView and
information on how to obtain the software and whom to
contact for assistance. It also contains the user
guide's table of contents and preface.
Chapter 2 (chapt2.ps)
Getting Started tells you how to set up your worksta-
tion environment and add XtalView to your path.
Chapter 3 (chapt3.ps)
Using XtalView gives an overview of the XtalView
software, including the crystal database, history
files, file formats, and plotting information. It also
tells you how to use the XView system, on which Xtal-
View is based.
Chapter 4 (chapt4.ps)
Programming XtalView gives programmers information for
adding other applications to XtalView and using the
XtalView database in other programs.
Chapters 5 and 6 (chapt5.ps, chapt6.ps)
contain reference pages for XtalView's window-based and
nonwindow-based applications. The information is organ-
ized into manual pages and listed in alphabetical
Release 3.0 of XtalView
colorbyb(1), cvtpdb(1), cvtvu(1), cvtxyz(1), deh(1),
deriv(1), dumpphasit(1), grinchbones(1), matrices(1),
mu2fin(1), resflt(1), stfact(1), urf2xfit(1), xcontur(1),
xdf(1), xedh(1), xfft(1), xfit(1), xheavy(1), xmerge(1),
xmergephs(1), xpatpred(1), xplortophs(1), xprepfin(1),
xresflt(1), xrspace(1), xtalmgr(1)