OASIS-2004 (CCP4 compatible)          Download the program OASIS-2004

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

  1. DESCRIPTION
  2. INPUT AND OUTPUT FILES
  3. KEYWORDED INPUT
  4. EXAMPLES
  5. AUTHOR
  6. 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

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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