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

Hao, Gu, Yao, Zheng & Fan (2001) in preparation.

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