xtalview



NAME

     xtalview - a suite of programs  for  solving  macromolecular
     crystal structures



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  (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 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-
               View

          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, 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
                    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  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
                    workstation.

                    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
                    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

     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
     manual.


     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
          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)