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