SAPI (CCP4: Supported Program)
NAMEsapi - A program to find heavy atom sites.
SYNOPSISsapi hklinfoo_in.mtz sapipks foo_sapi.pks
DESCRIPTIONSAPI 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.
INPUT AND OUTPUT FILESThe following input and output files are used 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)
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
AUTHORSY. 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.
Email: email@example.com or firstname.lastname@example.org