SAPI (CCP4: Supported Program)

NAME

   sapi - A program to find heavy atom sites.

SYNOPSIS

   sapi hklinfoo_in.mtz sapipks foo_sapi.pks
   [Keyworded input]

DESCRIPTION

   SAPI is a direct-method program to find heavy atom sites using
   one-wavelength anomalous scattering data or single isomorphous
   replacement  data. It can also be used to solve general small
   molecule structures.

   SAPI is run in two passes. The first run of SAPI is used to find
   list of sites, output in the SAPIPKS file.

   The second run is used to refine these sites and obtain scores
   using the KAR keyword. The output is again in the SAPIPKS file.
   NB. currently this requires copying the contents of the SAPIPKS
   file in the first job to the command script of the second.
   Also, because of the way that the SAPI input works, an EOF must
   occur before the input parsing occurs.

INPUT AND OUTPUT FILES

   The following input and output files are used by the program:

   Input Files:

   HKLIN
          Input MTZ file.
          This should contain the conventional (CCP4) asymmetric unit
          of data (preferably from TRUNCATE). See the LABIN keyword
          for columns used.

   Output Files:

   SAPIPKS
          Output  file  that contains the peak list found by the
          program.

KEYWORDED INPUT

   (The first three letters are significant except LABIN where the
   first four are necessary)

   The first keyword must be:

  TITLE <title string>

   The remaining keywords can be in any order. Some are compulsory
   (see individual descriptions).

   The possible keywords are:

     CELL, SPG, CON, KAR, LABIN, NRE, MAX, LIM, END

  CELL <a> <b> <c> <alpha> <beta> <gamma>

   (optional)
   Cell dimensions. If these are not given, cell dimensions will be
   read from the input MTZ file.

  SPG <space group>

   (optional)
   Space group (e.g. P 21 21 21); beware of the spaces in between. If
   this is not given, space group information will be read from the
   input MTZ file.

  CON <atom type> <number of atoms in unit cell >

   (optional)
   Contents of unit cell. If these are not known, the program will
   assume all carbon, and estimate the number according to the cell
   volume. Note: the program is not sensitive to the atom type, i.e.
   you may use C (carbon) to model anomalous scatterers such as Se.

  KAR <atom1> <x1> <y1> <z1> [<1> <occupancy1>] ...... <atom_n> <xn>
  <yn> <zn> [<n> <occupancy_n>]

   (optional)
   Fractional coordinates of atom(s). The coordinates will be refined
   by the Karle recycle method. An R-factor will be calculated to
   assess the quality of the given sites and additional sites can be
   found.

  LABIN DF=... SIGDF=...

   (compulsory)
   DF:
   Friedel   difference  (OAS)  or  the  isomorphous  difference
   |F(derivative)|-|F(native)| (SIR).

   SIGFD:
   standard deviation of DF.

  NRE <number>

   (optional)
   Number of largest E's used.

  MAX <number>

   (optional)
   Number of trials. (default = 1000).

  LIM <rmax> <rmin>

   Limits on data resolution in Angstrom (default: no low reso limit,
   3)

  END

   (compulsory)
   end of the keyword list

EXAMPLES

  The first run

     * sapi_run1.exam
       Example of SAPI locating Hg sites in rnase 25 data.
     *
#ompdc_1.com
sapi hklin ompdc.mtz sapipks ompdc_sapi.pks<<eof
TITLE   ompdc one-wavelength anomalous scattering data -
locating Se atoms
LABIN DF=DANO2 SIGDF=SIGDANO2
END
eof

  The second run

     * sapi_run2.exam
       Example of SAPI refining Hg sites in rnase 25 data.
     *
#ompdc_2.com
sapi hklin ompdc.mtz sapipks ompdc_sapi.pks<<eof
TITLE ompdc - refining the Se sites
labin DF=DANO2 SIGDF=SIGDANO2
KAR
      C    0.9481   0.0686    0.3858    1
      C    0.0501   0.1418    0.8754    2
      C    0.2278   0.0530    0.8609    3
      C    0.0996   0.0933    0.7587    4
      C    0.2879   0.1929    0.8885    5
      C    0.2921   0.2246    0.7965    6
      C    0.2016   0.2238    0.7753    7
      C    0.6243   0.2351    0.2025    8
      C    0.8794   0.0520    0.4618    9
      C    0.3525   0.1186    0.8852   10
      C    0.2272   0.1292    0.8899   11
      C    0.0386   0.0675    0.2715   12
      C    0.6741   0.2202    0.5788   13
      C    0.9896   0.0569    0.4514   14
      C    0.3682   0.0832    0.5957   15
      C    0.8689   0.0405    0.3536   16
      C    0.7619   0.1833    0.1968   17
      C    0.6529   0.2022    0.9082   18
END
eof

REFERENCES

    1. Q. Hao, Y. X. Gu, J. X. Yao, C. D. Zheng and H. F. Fan (2003)
       J. Appl. Cryst. 36 1274-1276. "SAPI: a direct-methods program
       for finding heavy-atom sites with SAD or SIR data."

AUTHORS

   Y. X. Gu (1), C. D. Zheng (1) & H. F. Fan (1) & Q. Hao (1, 2)

   (1) Institute of Physics, Chinese Academy of Sciences, Beijing
   100080, P. R. China.
   (2) MacCHESS, Wilson Synchrotron Lab, Cornell University, NY 14850,
   USA

   Email: qh22@cornell.edu or fan@aphy.iphy.ac.cn