xhercules

NAME

     xhercules - searches for heavy atom sites.

USAGE

     xhercules

DESCRIPTION

     xhercules searches for heavy atom sites by calling hercules.
     This  is  a brute force application of Patterson correlation
     methods. It is slow, but extremely robust.

MAIN WINDOW

     Crystal
          The  XtalView  crystal  keyword  accesses  the  crystal
          information file.


     Directory
          The current working directory.


     Fin File
          Fin file with merged native and derivative data.


     Solution File
          NONE for the first round,  then  solution  file  output
          from xheavy or xpatpred for the second round.


     Correlation Map
          The correlation map file (output in  xcontur/xfit  for-
          mat).


     Resolution Limits
          Set  the  resolution  maximum  and  minimum  limits  in
          angstroms on diffraction data.


     Search Grid
          The search grid     should be 1/4 to 1/6 resolution  in
          angstroms.


     X Bounds in Fractional
          Set the minimum and maximum bounds of x in fractions of
          unit cell (x asymmetric unit).

     Y Bounds in Fractional
          Set the minimum and maximum bounds of y in fractions of
          unit cell (y asymmetric unit).


     Z Bounds in Fractional
          Set the minimum and maximum bounds of z in fractions of
          unit cell (z asymmetric unit)


     Occupancy of Search Atom


     Search for Top Hit


     Cancel
          Stops running hercules.


     Top Hit
          Displays the top of the search.


     Append to Solution File
          Writes the top hit to the solution file.

          To search for an initial  site  enter  *NONE*  for  the
          solution  file  and select Search for Top Hit.  You can
          put this  initial  site  into  a  solution  file  using
          xpatpred.  Then, to search for a second site, enter the
          new solution file instead of  *NONE*  and  run  another
          search.   The  atom data in the solution file is in the
          same format as that used by xheavy.

          To guess an occupancy for the second site  relative  to
          the  first,  examine  the  Patterson map. It*s not very
          sensitive to the occupancy, so numbers like 1, .75, .5,
          or  .25  are  sufficient.  Use  xpatpred to display the
          predicted Patterson positions. To do  this,  enter  the
          site  and  then  write out a prediction file. Read this
          file into xcontur as a labels file. The vectors are put
          into the volume as 0-1, 0-1, 0-1, so they won*t show up
          on negative sections. For multiple site solutions,  pay
          particular  attention  to  the cross-peaks.  The search
          volume should be the asymmetric volume of the Patterson
          map.  The input format only allows for rectangular lim-
          its on asymmetric units. This may cause some  redundant
          computation  in  high symmetry space groups. For single
          sites there will be extra symmetry due to the fact that
          both  hands and all origin shifts are valid interpreta-
          tions of the Patterson map. For a second site there  is
          a  two-fold  ambiguity  due to the hand choice. You can
          reduce the search volume accordingly. If not, note that
          there  will  be  several equivalent hits (They will all
          give identical predictions with xpatpred). The solution
          can  then  be read directly into xheavy for refinement.
          If you want to use the PHASES package from Furey,  then
          xheavy can rewrite the solution into a file that*s more
          or less ready to use depending on  the  PHASES  version
          you  use.  hercules writes an fsfour style map that may
          be examined with xcontur. To  get  the  coordinates  in
          xcontur,  click  on  the  peaks. Sites are added to the
          solution file as they are  found  and  the  program  is
          rerun.  The  peaks  can  be  entered  into xpatpred and
          displayed on the Patterson map to verify their correct-
          ness.


          xhercules only takes a .fin file, not a .df  file.  You
          can  split off part of the data in a .df file to form a
          .fin file with awk. If you do this, you can extract the
          first entry in the .df file with the command:

          awk '{print $1, $2, $3, $4, $5, $6, $7}'  <  file.df  >
          file.fin

          You can extract the second entry with the command:

          awk '{print $1, $2, $3, $8, $9, $10, $11}' < file.df  >
          file.fin

          (For information about .fin and .df file  formats,  see
          Chapter 3 of the XtalView user guide.)

VERSION

     Release 3.2 of XtalView

SEE ALSO

     xtalview(1), hercules(1)