NAME
oasis04 - A direct-method program for ab initio phasing and
reciprocal-space fragment extension with SAD/SIR data
SYNOPSIS
oasis04 HKLIN foo_in.mtz HKLOUT
foo_out.mtz [XYZIN foo_in.pdb]
[Keyworded input]
CONTENTS
- DESCRIPTION
- INPUT AND OUTPUT FILES
- KEYWORDED INPUT
- EXAMPLES
- AUTHOR
- REFERENCES
DESCRIPTION
OASIS-2004 is a computer program of phasing One-wavelength Anomalous
Scattering or Single Isomorphous Substitution
(Replacement) protein data. The phase problem is reduced to a sign problem once
the anomalous-scatterer or the replacing-heavy-atom sites are located. OASIS-2004
applies a direct method procedure to solve this sign problem. It also possesses
the function of reciprocal-space fragment extension using SAD/SIR data. This is
particularly useful when the total conribution of known fragments is not large
ennough for Fourier recycling.
INPUT AND OUTPUT FILES
The input files include the keyword file, the CCP4 MTZ reflection data file and,
if available, the standard PDB file containing known structure fragment(s).
Input Files:
HKLIN
Input data file (MTZ).
XYZIN
Input fragment file (PDB). This file is usually obtained from
automatic model building programs. The file should contain the CRYST and SCALE
information at the beginning.
Output Files:
HKLOUT
- Output data file (MTZ).
KEYWORDED INPUT
The possible keywords are:
LABIN,
TIT,
CON,
COS,
FOM,
AOE,
KMI,
CYC,
ANO,
POS,
FRA,
SAD/SIR,
LIM
LABIN FP=... SIGFP=... [FPH=... SIGFPH=...] DANO=...
SIGDANO=... [PHIC=...]
(compulsory)
- FP, SIGFP:
- averaged structure-factor magnitude [F(+) + F(-)]/2 of SAD data or
Fobs of the native protein of SIR data and its standard deviation.
FPH, SIGFPH:
- Fobs of the derivative of SIR data and its standard deviation.
- DANO, SIGDANO:
- Bijvoet difference, F(+) - F(-), of SAD data and its standard deviation.
- PHIC:
- standard phase for comparison with the resultant phase
- F(+), SIGF(+), F(-), SIGF(-):
- structure factor amplitudes for hkl and its Friedel mate -h-k-l.
The acceptable formats for SAD/SIR phasing as followings:
- SIR phasing:
- LABIN FP=... SIGFP=... FPH=... SIGFPH=... [PHIC=...]
- SAD phasing:
- LABIN FP=... SIGFP=... DANO=... SIGDANO=... [PHIC=...]
- or
- LABIN F(+)=... SIGF(+)=... F(-)=... SIGF(-)=... [PHIC=...]
Note: If the keyword LABIN is missing, the program will assume that SAD data
with the format
"FP=FP SIGFP=SIGFP DANO=DANO SIGDANO=SIGDANO"
are to be input. Any conflictions to this will result in errors.
TIT <title string>
(optional)
Job title, up to 80 characters.
CON <atom
type> <number of atoms in ASU >
(compulsory)
Example:
CON C 770 N 185 O 231 H 1232 CU 1
This keyword specifies the contents in the asymmetric unit, which can be
approximately estimated as follows:
Let r be the number of residues in the asymmetric unit, then the contents
will be C 5r, N 1.2r, O 1.5r, H 8r plus atoms other
than the above chemical elements.
COS
(optional)
By default, after calculating COS(delta_phi) values from the measured Bijvoet
differences, the program will modify the resultant COS(delta_phi)'s to fit them
in the uniform distribution from 1 to -1. This will cope with sharp deviations due
to experimental errors. The keyword COS informs the program NOT to fit the
COS(delta_phi) values in the uniform distribution. Instead, the program will not
change the COS(delta_phi) values if they are within the range of 1 to -1. Besides,
All values greater than 1 will be cut to 1. All values smaller than -1 will be set
as -1. It is NOT recommended to use the keyword COS in most cases except when you
are very confident about the measured Bijvoet differences.
FOM
(optional)
By default the output figures-of-merit for individual reflections will be fitted
to the uniform distribution from 0 to 1. Usually this leads to a better
electron-density map for the subsequent density modification. The keyword FOM
informs the program to turn off this function. This is provided for use when the
user is unsatisfied with the default phasing result.
AOE <value>
(optional)
By default the average value of EXP[-(sigma_H)**2/2] in the P+ formula will be
tuned automatically to 0.5. The user can use the keyword AOE to set the tuned
average EXP[-(sigma_H)**2/2] to other values within the range of 0 to 1.
KMI <value>
(compulsory).
This keyword specifies the minimum kappa value of three-phase structure invariants
accepted in direct-method phasing. The small is the KMI value, the large is the
number of structure invariants that will be involved in the phasing process and,
the reliable will be the phasing results. A KMI value of 0.03 would usually lead
to a pretty good result, while a value of 0.01 may in most cases even better.
However, for a big protein, a KMI of 0.01 may cause problems in computing time or
even in computer storage. It is recommended to check the total number of
three-phase structure invariants (phase relationships) output by the
program and adjust the value of kappa minimum accordingly so as the total number
of structure invarinats is kept within the range of 10,000,000 ~ 50,000,000 or not
exceeds the capacity of your computer.
CYC <ncycle>
(optional)
Number of cycles for P+ formula iteration (default: 2).
ANO <atom> <f">
(compulsory in SAD case)
chemical symbol of the anomalous scatterer and the corresponding f" value - the
imaginary-part correction to the atomic scattering factor
Example:
ANO HG 7.686
ZN 0.678
POS <atom_1> <1>
<x_1> <y_1> <z_1>
<occupancy_1> <bfactor_1>
.
.
.
<atom_n> <n>
<x_n> <y_n> <z_n>
<occupancy_n> <bfactor_n>
(compulsory)
Fractional coordinates of anomalous scatterer(s) or replacing heavy atom(s)
in the asymmetric unit.
FRA <atom_1> <1>
<x_1> <y_1> <z_1>
<occupancy_1> <bfactor_1>
.
.
.
<atom_n> <n>
<x_n> <y_n> <z_n>
<occupancy_n> <bfactor_n>
(optional)
This keyword specifies atomic parameters of the structure fragment(s)
(in fractional coordinates in the asymmetric unit) for
partial-structure iteration when the PDB file is not available.
SAD/SIR
(compulsory)
This specifies that SAD phasing or SIR phasing is to be performed.
LIM <dmin>
(optional)
This specifies the high resolution cutoff in Angstroms (default: no cutoff).
EXAMPLES
Runnable examples
a. Examples of OAS/SAD phasing:
b. Example of SIR phasing:
Example 1:
[Ab initio phasing of SAD data]
#!/bin/csh -f
oasis04 \
hklin rusti.mtz \
hklout rusti_oasis.mtz << +
LABIN FP=FP SIGFP=SIGFP DANO=DANO SIGDANO=SIGDANO PHIC=PHICalc
TIT Ab initio phasing of Rusticyanin SAD data
CON C 770 N 185 O 231 H 1232 CU 1
KMI 0.01
ANO CU 3.8790
POS
CU 1 0.1506 0.2500 0.4265 0.8531 12.8654
SAD
+
Example 2:
[Fragment extension with SAD data]
#!/bin/csh -f
oasis04 \
hklin rusti.mtz \
hklout rusti_oasis.mtz \
xyzin resolve_build.pdb << +
LABIN FP=FP SIGFP=SIGFP DANO=DANO SIGDANO=SIGDANO
TIT Fragment extension with Rusticyanin SAD data
CON C 770 N 185 O 231 H 1232 CU 1
KMI 0.01
ANO CU 3.8790
POS
CU 1 0.1506 0.2500 0.4265 0.8531 12.8654
SAD
+
Example 3: [Phasing
SAD data and comparing resultant phases with known phases]
#!/bin/csh -f
oasis04 \
hklin rusti.mtz \
hklout rusti_oasis.mtz << +
LABIN FP=FP SIGFP=SIGFP DANO=DANO SIGDANO=SIGDANO PHIC=PHICalc
TIT Phasing Rusticyanin SAD data
CON C 770 N 185 O 231 H 1232 CU 1
KMI 0.01
ANO CU 3.8790
POS
CU 1 0.1506 0.2500 0.4265 0.8531 12.8654
SAD
+
Example 4: [Phasing
SIR data and comparing resultant phases with known phases]
#!/bin/csh -f
oasis04 \
hklin rnase25_sfall.mtz \
hklout rnase25_oasis_0.mtz << +
LABIN FP=FNAT SIGFP=SIGFNAT FPH=FPTNCD25 SIGFPH=SIGFPTNCD25 PHIC=PHICalc
TIT Phasing RNASE SIR data
CON C 970 N 233 O 291 H 1552 PT 5
KMI 0.01
POS
PT 1 0.1571 0.4433 0.0318 0.5628 33.1670
PT 2 0.3081 -0.0049 0.2439 0.5145 35.7061
PT 3 -0.4332 -0.1725 0.0193 0.6404 34.3959
PT 4 0.1022 -0.0592 0.1848 0.4491 32.7726
PT 5 -0.0495 0.3444 0.2246 0.2106 21.4640
SIR
+
AUTHORS
Jia-wei Wang, Yuan-xin Gu, Chao-de Zheng, & Hai-fu Fan
Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China
and
Quan Hao
MacCHESS, 273 Wilson Synchrotron Lab, Cornell University, Ithaca,
NY 14853-8001, U.S.A.
Email: fan@mail.iphy.ac.cn
or gu@cryst.iphy.ac.cn
REFERENCES
- Fan, H. F. & 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.
- Fan, H. F., Hao, Q., Gu, Y. X., Qian, J. Z., Zheng, C. D. & 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.
- Hao, Q., Gu, Y. X., Zheng, C. D. & Fan, H. F. (2000). "OASIS: a program
for breaking phase ambiguity in OAS or SIR". J. Appl. Cryst.
33, 980-981.
- Wang, J. W., Chen, J. R., Gu, Y. X., Zheng, C. D., Jiang, F. & Fan, H. F.
(2004). "Optimizing the error term in direct-method SAD phasing".
Acta Cryst. D60, 1987-1990.
- Wang, J. W., Chen, J. R., Gu, Y. X., Zheng, C. D. & Fan, H. F. (2004).
"Direct-method SAD phasing with partial-structure iteration - towards automation".
Acta Cryst. D60, 1991-1996.
* PDF files of papers in the REFERENCES are available on
http://cryst.iphy.ac.cn