XtalView

Users' Guide at The Computational Center for MacroMolecular Structures (CCMS), click here


XtalView - a suite of programs for solving macromolecular crystal structures

http://www.scripps.edu/pub/dem-web/index.html

XtalView Guide (pdf)

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 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@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@sdsc.edu leave the SUBJECT line blank type ' get xtalview ' in the message

For technical support, or any other questions, contact CCMS at ccms-help@sdsc.edu (email) or (619)534-5100 (telephone)

SETTING UP THE XTALVIEW ENVIRONMENT

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

    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

    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 make use of 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 direc- tories to the font path, you must also move any 100dpi directories to the end of the font path. 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)). NOTE Silicon Graphics users should read the file $XTALVIEWHOME/make_sgi4dIRIX4/README for additional instruc- tions.

DOCUMENTATION

XtalView User's Guide is at:

http://www.sdsc.edu/CCMS/Packages/XTALVIEW/XVcpyrt.html

Contents

Preface

Chapter 1 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 Getting Started tells you how to set up your workstation environment and add XtalView to your path.

Chapter 3 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 XtalView is based.

Chapter 4 Programming XtalView gives programmers information for adding other applications to XtalView and using the XtalView database in other programs.

Chapters 5 and 6 contain reference pages for XtalView's window-based and nonwindow-based applications. The information is organized into manual pages and listed in alphabetical order.

VERSION

Release 3.0 of XtalView

SEE ALSO

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)