xmergephs

NAME

     xmergephs - merge fin and phase  files;   phase  derivatives
     and mutants.

USAGE

     xmergephs fin_file phs_file

DESCRIPTION

     The data in fin_file is phased with the phases  in  phs_file
     and  the  resultant  structure  factors  are  written out in
     another phase file.  The phase file can  be  either  a  .phs
     file,  an  XPLOR phase file, or a TNT hkl file.  Options are
     available for using  isomorphous or Bijvoet differences.


     Quit The normal quit button.


     Directory
          The directory.


     Fin File to Phase
          The fin file to be  phased  (h  k  l  f1  sigma(f1)  f2
          sigma(f2)).


     Phase File
          The file with phases to be used  for  phasing  the  fin
          file  can  be  either a .phs file, an XPLOR format file
          with the entry FCALC=, or a TNT hkl format  file.   The
          phase  is  normally expected to be in degrees, although
          if you use xfft in the next step radians are OK.


     Output Phase File
          The output is written to this  file.   The  f1  and  f2
          fields  in the fin file are written out h k l f1 f2 phi
          unless otherwise specified (see below).


     Swap f1 and f2 (isomorphous Fourier)
          If f1 is the native FP in your fin file and f2  is  the
          derivative  FPH,  then  f1  and f2 should be swapped so
          that the output is h k l  FPH  FP  phi,  and  then  you
          should  make  an fo-fc Fourier map, which will show the
          positions of the heavy atoms if protein phases are used
          (double difference Fourier).

          You may also want to swap mutant  data  that  has  been
          merged  with  native  data  to  make  a Fmutant-Fnative
          difference Fourier.


     Add 90 to phase (Bijvoet Fourier)
          If the fin file contains Bijvoet differences (h k l  f+
          sigma(f+)  f-  sigma(f-))  and the input phases were in
          degrees then a Bijvoet difference Fourier can  be  made
          by adding 90 to the phase and swapping f1 and f2.  Cen-
          tric reflections will be handled correctly if they have
          0.0  in  the f- position. If you have used XtalView the
          whole way and started with a XENGEN mu file  then  they
          will be correct.  If f+ is equal to f- then the reflec-
          tions will be output but since their difference is zero
          they will not contribute to the Fourier.


     Merge
          Click here when you are ready to go.  The  program  can
          take  quite  a  long time if the two input files have a
          different  sort  order  as  the  program  searches  for
          matches in indices between the two programs.  Note that
          if you have equivalent indices that are not numerically
          the same (e.g. h k l and -h -k l) the merge will fail!

BUGS

     The aforementioned problem, if the  indices  are  equivalent
     but not identical, causes the program to not find a match.

VERSION

     Release 3.2 of XtalView

SEE ALSO

     xtalview(1)