SAPI (CCP4 supported program)

NAME

sapi - A program to find heavy atom sites.

Source Code

sapi.f (SHIFT click to save on disk)
To compile: f77 -o sapi sapi.f -L$CCP4_LIB -lccp4
On a Linux box, use: f77 -o sapi -static -fno-second-underscore -fno-globals sapi.f -L$CCP4_LIB -lccp4

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.

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).

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 ]

#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]

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

AUTHORS

YX Gu, JX Yao, CD Zheng, HF Fan &
 Institute of Physics, Chinese Academy of Sciences, Beijing 100080, P. R. China.
Q Hao
Cornell University, USA.
Email: qh22@cornell.edu  or  fan@aphy.iphy.ac.cn