deriv

NAME

     deriv - calculate the derivative of a difference map at each
     atom.

USAGE

     deriv file.pdb refl.phs out.vu [resmin] [resmax]

DESCRIPTION

     The input is a PDB file (.pdb) and a phase file  (.phs)  and
     the  output  is  a  vu  file,  suitable for xfit, containing
     arrows showing the direction and relative magnitude  of  the
     gradient.  If  one resolution limit is given then it is con-
     sidered the  minimum  resolution.  If  two  are  given  data
     between  them  are  used,  and if none are given all data is
     used.

PURPOSE

     This function is also provided within xfit.   It  calculates
     the derivative of the difference electron density of the two
     amplitudes given in the phase file.  If  the  file  contains
     Fobs and Fcalc this is Fobs-Fcalc.  Another useful construct
     is Fmutant-Fnative.  An arrow is drawn at this  position  in
     the direction of the gradient of the difference map with the
     length indicating the steepness normalized for the atom type
     (do not take these literally, they are only relative indica-
     tors).  This is the direction  a  refinement  program  would
     move  the atom in the first cycle if no stereochemistry were
     taken into account.  Also, this is not very useful at  reso-
     lutions  far  from atomic resolution (say below 2.5A).  This
     program is provided for those who want to use it  with  some
     other   program   (converting   the   vu   file   is   their
     responsibility--remember it is x1 y1 z1 x2 y2 z2 color), and
     also  because  performing  this  calculation  for  an entire
     molecule would take quite a long time and  would  stop  xfit
     while  it  was  being  done.   Since xfit does not provide a
     mechanism for saving the vectors it calculates, if you  will
     be  using  them  over  several  sessions they should be pre-
     calculated with deriv.

VERSION

     Release 3.2 of XtalView

SEE ALSO

     xtalview(1), xfit(1)