OASIS (CCP4: Supported Program)

NAME

oasis - A program for breaking phase ambiguity in OAS or SIR

SYNOPSIS

oasis hklinfoo_in.mtz hkloutfoo_out.mtz
[Keyworded input]

DESCRIPTION

OASIS is a computer program for breaking phase ambiguity in One-wavelength Anomalous Scattering or Single Isomorphous Replacement (Substitution) protein data. The phase problem is reduced to a sign problem once the anomalous-scatterer or the replacing-heavy-atom sites are located. OASIS applies a direct method procedure to break the phase ambiguity intrinsic to OAS or SIR data.

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:
HKLOUT
Output MTZ file.

See the LABOUT keyword for columns output.

KEYWORDED INPUT

(The first three letters are significant except LABI and LABO 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, HCO, FIT, LCE, KMI, CYC, OAS/SIR, ANO, POS, PHI, LABIN, LABOUT, RES, SIG, 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. 

HCO <heavy atom type> <number of heavy atoms in unit cell>

(compulsory)
Type and number of heavy atoms in the unit cell (not just the asymmetric unit). 

FIT

(optional)
FIT will force the cos(delta phi)'s to follow a uniform distribution. This will cope with sharp deviations due to experimental errors in DANO. It is recommended for most cases except when you are very confident about your DANO (column F2 of the LABIN keyword). 

LCE <value>

(optional)
Lack of closure error - an important component in the figure of merit (FOM). Suggested values: 20 for 'heavier' heavy atoms, e.g. Hg, Pt; 7 for 'lighter' heavy atoms, e.g. Cu, Fe. Any negative value will force the FOM to follow a uniform distribution.
(default: -7) 

KMI <value>

(optional)
sigma-2 relationship kappa value cutoff
(default: 0.05) 

CYC <ncycle>

(optional)
number of cycles, recommended number for OAS data: 1
(default: 1) 

OAS | SIR

(optional)
One-wavelength Anomalous Scattering or Single Isomorphous Replacement data
(default: OAS) 

ANO <atom> <f">

(compulsory in OAS case)
f" value of the anomalous scatterer. Given the wavelength, this can be computed using CROSSEC. 

POS <atom1> <x1> <y1> <z1> [<1> <occupancy1>] ...... <atom_n> <xn> <yn> <zn> [<n> <occupancy_n>]

(compulsory)
Fractional coordinates of anomalous scatterer(s) --- heavy atom(s). 

Note you must provide coordinates for scatterers in the asymmetric unit only i.e. not the unit cell. (Note that this is different to the HCO and CON keywords, which do require the numbers in the unit cell.)

PHI

(optional)
Phase comparison with known phases. The latter are taken from HKLIN, see LABIN keyword. 

LABIN F1=... SIGF1=... F2=... SIGF2=... [TPHI=...]

(compulsory)
F1:
mean F magnitude (OAS) or native F magnitude (SIR)
SIGF1:
standard deviation of F1
F2:
Friedel difference (OAS) or the isomorphous difference |F(derivative)|-|F(native)| (SIR). Must be column type D.
SIGF2:
standard deviation of F2.
TPHI:
phase to be compared with (only required when PHI keyword is present)

LABOUT F1=... SIGF1=... PHI=... W=...

(optional)
F1:
as input
SIGF1:
as input
PHI:
derived phase
W:
weight attached to PHI

RES <rmin>

(optional)
High resolution cutoff in Angstrom.
(default: no cutoff) 

SIG <Nsig>

(optional)
Reflections will be excluded if F1 < Nsig*SIGF1.
(default: no reflections are excluded) 

END

end of the keyword list

EXAMPLES

Runnable examples using rnase data

Other examples

[direct phasing of OAS data] 
#rc9.com
 oasis hklin rc9.mtz hklout rc9.out.mtz <<eof
*** DIRECT PHASING OF rc9 OAS DATA ***
CEL 32.43 60.68 38.01 90.00 107.82 90.00
CON C  2000   N  300   O  400  CU 2
HCO CU 2
SPG P 21
FIT
LCE 7
KMIN 0.05
CYC 1
ANO CU 3.879
POS   CU  0.1474 0.25 0.4228
LABIN F1=FP SIGF1=SIGFP F2=DANO SIGF2=SIGDANO
LABOUT F1=FP SIGF1=SIGFP PHI=PHIdp W=Wdp
END
eof
[ direct phasing of OAS data and comparing phase error with model phases] 
#az.com
 oasis hklin az.mtz hklout az1.out.mtz <<eof
*** DIRECT PHASING OF CU-AZURIN OAS DATA ***
CEL 52.65 52.65 100.63 90.00 90.00 90.00
CON C  6400   N  800   O  1200   CU 8
HCO CU 8
SPG P 41 2 2
PHI
FIT
LCE 7
KMIN 0.05
CYC 1
ANO CU 1.900
POS CU  0.1827   0.1395  0.2498
LABIN F1=FP SIGF1=SIGFP F2=DANO SIGF2=SIGDANO TPHI=PHIT
LABOUT F1=FP SIGF1=SIGFP PHI=PHIdp W=Wdp
END
eof
[ direct phasing of SIR data and comparing phase error with model phases] 
#rnase.com
oasis hklin rnase.mtz hklout rnase.out.mtz <<eof
*** DIRECT PHASING OF RNASE SIR DATA ***
CEL 64.90 78.32 38.79 90.00 90.00 90.00
CON C  3720   N  976   O  2240   S  28 PT 6
HCO PT 6
SPG P 21 21 21
PHI
FIT
LCE 20
KMI 0.10
CYC 1
SIR
POS PT     0.567   0.829   0.018     1       0.416
    PT     0.842   0.945   0.467     2       0.335
    PT     0.103   0.940   0.194     3       0.310
    PT     0.190   0.006   0.744     4       0.282
    PT     0.047   0.852   0.277     5       0.179
LABIN F1=AMP SIGF1=SIGAMP F2=SIRDIF TPHI=PHA
LABOUT F1=FP SIGF1=SIGFP PHI=PHIdp W=Wdp
END

SEE ALSO

mlphare - MIR/MAD phasing
dm - density modification

REFERENCES

  1. Hao, Q.*, Gu, Y.X., Zheng, C.D. & Fan, H.F. (2000) J. Appl. Cryst. 33, 980-981. "OASIS: A Program for Breaking Phase Ambiguity in OAS or SIR".
  2. Fan, H. F. and Gu, Y. X. (1985) Combining direct methods with isomorphous replacement or anomalous scattering data III. The incorporation of partial structure information, Acta Cryst. A41, 280-284.
  3. Fan H. F., Hao, Q., Gu, Y. X., Qian, J. Z., Zheng, C. D. and Ke, H. (1990) Combining direct methods with isomorphous replacement or anomalous scattering data VII. Ab initio phasing of the OAS data from a small protein, Acta Cryst. A46, 935-939.
  4. Y. -D. Liu, I. Harvey, Y. -X. Gu, C. -D. Zheng, Y. -Z. He, H. -F. Fan, S. S. Hasnain and Q. Hao (1999) Is single-wavelength anomalous scattering sufficient for solving phases? A comparison of different methods for a 2.1 A structure solution, Acta Cryst. D55, 1620-1622.

AUTHORS

Q. Hao (1, 2), Y. X. Gu, C. D. Zheng & H. F. Fan (2)

(1) MacCHESS, Wilson Synchrotron Lab, Cornell University, NY 14850, USA
(2) Institute of Physics, Chinese Academy of Sciences, Beijing 100080, P. R. China.

Email: qh22@cornell.edu or fan@aphy.iphy.ac.cn