OASIS (CCP4: Supported Program)

NAME

oasis - a direct-methods program for SAD/SIR phasing and reciprocal-space fragment extension

SYNOPSIS

oasis 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. AUTHORS
  6. REFERENCES

DESCRIPTION

OASIS-2006 is a computer program for ab initio SAD/SIR phasing and reciprocal-space fragment extension. The phase problem is reduced to a sign problem once the anomalous-scatterer or the heavy-atom substitution sites are located. The sign problem is then solved by a direct method. OASIS-2006 also performs reciprocal-space fragment extension with or without SAD/SIR information. This is particularly useful when the total contribution of known fragments is not large enough for Fourier recycling.

INPUT AND OUTPUT FILES

HKLIN
Input data file (CCP4 mtz format).
XYZIN (optional)
This is a .pdb file for providing partial structure information, which is usually obtained from automatic model building programs. The file should contain CRYST and SCALE information at the beginning. Dummy atoms will be rejected in subsequent processing.
FRCIN (optional)
This file contains partial structure information extracted from a *.pdb file using the script pdb2frc.csh. Atomic positional parameters are converted to fractional coordinates. Dummy atoms will be reserved and assigned as carbon atoms.
HKLOUT
Output data file (CCP4 mtz format).

KEYWORDED INPUT

The possible keywords are:

TIT, SAD/SIR/DMR, LABIN, CON, COS, FOM, AOE, KMI, CYC, ANO, POS, FRA, NHA, SED, LIM

TIT <title string>

(optional)
This keyword creates a job-title string, which consists of up to 80 characters.

SAD/SIR/DMR

(compulsory)
This specifies the calculation mode:
SAD
Ab initio phasing or fragment extension with SAD data
SIR
Ab initio phasing or fragment extension with SIR data
DMR
Fragment extension without SAD/SIR information. This can be used as Direct-method MR-model completion with native data in the absence of SAD signals.

LABIN FP=... SIGFP=... [FPH=... SIGFPH=...] DANO=... SIGDANO=... [PHIC=...]

(compulsory)
FP, SIGFP:
averaged structure-factor magnitude [F(+) + F(-)]/2 and its standard deviation in SAD mode;
Fobs of the native protein and its standard deviation in SIR or DMR mode.
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 different calculation modes are as follows:

SAD:
LABIN FP=...  SIGFP=...  DANO=...  SIGDANO=...  [PHIC=...]

   or

LABIN F(+)=...  SIGF(+)=...  F(-)=...  SIGF(-)=...  [PHIC=...]
SIR:
LABIN FP=...  SIGFP=...  FPH=...  SIGFPH=...  [PHIC=...]
DMR:
LABIN FP=...  SIGFP=...  [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 departures from this will result in errors.


CON <atom type> <number of atoms in ASU >

(compulsory)
Example: 

  CON    C 770   N 185   O 231   H 1232   CU 1

This keyword specifies 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.
An alternative and more accurate way to calculate contents in asymmetric unit is to run the script seq2con.csh with the sequence file by issuing the command: seq2con.csh name.pir


COS

(optional)
By default, COS(delta_phi) values calculated from experimental Bijvoet differences will be modified to obey uniform distribution within the range of 1 to -1. This will cope with large experimental errors. The keyword COS informs the program NOT to fit COS(delta_phi) values to uniform distribution. Instead, COS(delta_phi) values within the range of 1 to -1 will be kept unchanged and, values greater than 1 will be cut to 1 while values smaller than -1 will be set to -1. It is NOT recommended to use the keyword COS 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 so as they are uniformly distributed 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 smaller the KMI value, the larger the number of structure invariants involved in the phasing process and the more reliable the phasing results. A KMI value of 0.03 would usually lead to a satisfactory result, while a value of 0.01 may in most cases be even better. However, for a big protein, a KMI of 0.01 may cause problems in computing time. 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 invariants is kept within the range of 10,000,000 ~ 50,000,000.

CYC <ncycle>

(optional)
Number of cycles for P+ formula iteration (default: 2).

ANO <atom> <f">

(compulsory in SAD mode)
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
The script crossec.csh can help with calculating anomalous corrections, for example the command: crossec.csh Br 0.9191 will calculate anomalous corrections to the atomic scattering factor of Br at the wavelength of 0.9191Å.


POS   <atom_1>   <1>   <x_1>   <y_1>   <z_1>     <occupancy_1>   <B-factor_1>
                .
                .
                .
          <atom_n>   <n>   <x_n>   <y_n>   <z_n>     <occupancy_n>   <B-factor_n>

(compulsory in SAD/SIR mode)
Fractional coordinates of anomalous scatterer(s) or replacement heavy atom(s) in the asymmetric unit.


FRA   <atom_1>   <1>   <x_1>   <y_1>   <z_1>     <occupancy_1>   <B-factor_1>
                .
                .
                .
          <atom_n>   <n>   <x_n>   <y_n>   <z_n>     <occupancy_n>   <B-factor_n>

(optional)
This keyword specifies atomic parameters of the known fragment(s) (in fractional coordinates in the asymmetric unit) for partial-structure iteration when the PDB file is not provided.

NHA <value>

(optional in DMR mode)
This specifies the percentage of atoms to be included in artificial partial structure (default: 5).

SED <value>

(optional in DMR mode)
This specifies the seed value of the random-number generator used for creating artificial partial structure (default: 1).

LIM <dmin>

(optional)
This specifies the high resolution cutoff in Angstroms for reflections involved in the calculation (default: no cutoff).

 
 
 

EXAMPLES

Runnable examples

a. Examples of SAD phasing:

b. Example of MR-model completion:


Example 1: [Ab initio SAD phasing]

#!/bin/csh -f
oasis06 hklin pscp.mtz hklout pscp_oasis_1.mtz << +
TIT Ab initio SAD phasing of pscp
SAD
LABIN FP=FP SIGFP=SIGFP DANO=DANO SIGDANO=SIGDANO
CON C 1683 N 458 O 571 BR 9 S 3
KMI 0.03
ANO BR 3.8143
POS
BR 1 0.63036 0.20655 0.00000 0.42 14.700
BR 2 0.50000 0.00000 0.00716 0.28 14.400
BR 3 0.14603 0.42154 0.25609 0.44 29.700
BR 4 0.44531 0.41895 0.24849 0.19 3.700
BR 5 0.90769 0.26779 0.02868 0.39 30.700
BR 6 0.69134 0.20471 0.27918 0.38 30.200
BR 7 0.59988 0.42259 0.11135 0.36 25.000
BR 8 0.65702 0.37410 0.06040 0.33 25.500
BR 9 0.69461 0.39047 0.25676 0.26 20.100
+

Example 2: [Fragment extension with SAD data]

#!/bin/csh -f
oasis06 hklin azurin.mtz frcin azurin_1.frc hklout azurin_1_oasis.mtz << +
TIT Fragment extension with azurin SAD data
SAD
LABIN FP=FP SIGFP=SIGFP DANO=DANO SIGDANO=SIGDANO
CON C 600 N 165 O 185 S 10 CU 1
ANO CU 2.168
POS
   CU 1 0.1401 0.8162 -0.0021 1.0 11.7852
KMI 0.02
+

Example 3: [MR-model completion without SAD/SIR information]

#!/bin/csh -f
oasis06 hklin 0_start.mtz frcin 0_start.frc hklout 1ujz_1_oasis.mtz << +
TIT MR-model completion of 1ujz
DMR
NHA 5
SED 9
LABIN FP=FP SIGFP=SIGFP
CON C 1086 N 312 O 334 S 3
COS
FOM
KMI 0.05
+

AUTHORS

Tao Zhang, Yao He, Yuan-xin Gu, Chao-de Zheng, Jia-wei Wang & Hai-fu Fan
Beijing National Laboratory for Condensed Matter Physics,
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.

Emails: gu@cryst.iphy.ac.cn; fanhf@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. 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.
  3. 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.
  4. He, Y., Yao, D.Q., Gu, Y.X., Lin, Z.J., Zheng, C.D. & Fan, H.F. (2007). "OASIS and MR-model completion". Acta Cryst. D63 (in the press).
  5. He, Y., Gu, Y.X., Lin, Z.J., Zheng, C.D. & Fan, H.F. (2007). "SIR phasing by combination of SOLVE/RESOLVE and dual-space fragment extension". (To be published)
  6. Zhang, T., He, Y., Gu, Y.X., Zheng, C.D. Hao, Q., Wang, J.W. & Fan, H.F. (2007). "OASIS-2006, a direct-methods program for SAD/SIR phasing and reciprocal-space fragment extension". (To be published).

* PDF files of papers in the REFERENCES are available on http://cryst.iphy.ac.cn