SAPI (CCP4: Supported Program)
sapi - A program to find heavy atom sites.
sapi hklinfoo_in.mtz sapipks foo_sapi.pks
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 MTZ file.
This should contain the conventional (CCP4) asymmetric unit of data (preferably
from TRUNCATE). See the LABIN
keyword for columns used.
Output file that contains the peak list found by the program.
(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
The possible keywords are:
CELL <a> <b> <c> <alpha> <beta> <gamma>
Cell dimensions. If these are not given, cell dimensions will be read
from the input MTZ file.
SPG <space group>
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
CON <atom type> <number of atoms in unit cell >
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>]
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=...
Friedel difference (OAS) or the isomorphous difference |F(derivative)|-|F(native)|
standard deviation of DF.
Number of largest E's used.
Number of trials. (default = 1000).
LIM <rmax> <rmin>
Limits on data resolution in Angstrom (default: no low reso limit, 3)
end of the keyword list
The first run
The second run
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."
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: firstname.lastname@example.org or email@example.com