DECONV - DECONVOLUTE MULTIPLES

INTRODUCTION

List of sections:

Structure
Input and Output Files
Running the Programs
References
Examples

STRUCTURE

The package consists of seven programs. Two of them (FFT, SFALL) come from the standard CCP4 package (see ref 1) and one (LAUENORM) from the LAUE suite. They are as follows:

1. DECONV_PREP

   Prepare .mtz files for multiples.

2. FFT

   Calculate a Patterson map with reflection intensities of singles evaluated by the previous run of the LAUE suite.

3. DECONV_MMOD

   Modify this map.

4. SFALL

   Calculate Fourier coefficients of the multiples with the modified map.

5. DECONV_DCON

   Evaluate Laue diffraction intensities of multiples.

6. LAUENORM

   Perform a wavelength normalisation using lambda-curve determined by singles.

7. DECONV_COMB

   Ccombine singles and multiples for output

INPUT AND OUTPUT FILES

Each program (except DECONV_COMB) requires a Data Control File (in free format). However, DECONV_PREP and DECONV_DCON use the same file.

The input files are:

1. Control file for FFT

   This is a keyworded file (see CCP4 documentation for further details.

   The items required are:

   1. TITLE title

      Up to 80 character title for map.

   2. LABIN F1=F

      MTZ assignment for the input MTZ reflection data file.

   3. SCALE F1 scale b

      Scale (scale) and temperature (b) factors to be applied on F.

   4. VF000 v f000

      Unit cell volume (v) and F000 value (f000).

   5. PATTERSON

      Instruction to calculate the Patterson map.

   6. GRID nx ny nz

      Number of sampling divisions along whole cell edge.

   7. AXIS Y X Z or Z X Y

      Axis order fast, medium, slow. Y X Z for Trigonal and Hexagonal space groups; Z X Y for other space groups (treated as P1).

   8. XYZLIM 0 nx-1 0 ny-1 0 zmax

      Range of cell to be calculted. zmax=nz/3-1 (Trigonal); zmax=nz/6-1 (Hexagonal); and zmax=nz-1 (all other space groups).

2. Control file for DECONV_MMOD

   The items required are:

   1. TITLE

      Up to 80 character title for map modification

   2. RHOMIN POWER RHOMAX

      RHOMIN, RHOMAX: lower and upper limits of the modified map (set to zero to get default values).

      POWER: map to be modified by rho**{POWER).

3. Control file for SFALL

   This is a keyworded file (see CCP4 documentation for further details.

   The items required are:

   1. TITLE title

      Up to 80 character title for structure factor calculation.

   2. MODE SFCALC MAPIN HKLIN

      Mode indicating structure factor calculation.

   3. GRID nx ny nz

      Same as FFT.

   4. RESO dmin dmax

      Resolution limits in Angstrom.

   5. NOSCAL

      No scale factor to be applied to output structure factors.

   6. SFSG 1

      Space group number used to calculate structure factors (NOT required for Trigonal and Hexagonal).

   7. LABIN FP=F SIGFP=SIGF

      MTZ assignment for the input MTZ reflection data file.

   8. LABOUT FC=FC PHIC=PHIC

      MTZ assignment for the output MTZ reflection data file.

   9. END

      End of control file.

4. Control file for DECONV_PREP and DECONV_DCON

   The items required are:

   1. NCOMM

      Flag indicating how Victorian Coefficients (VC) to be input:

      =0, single image plate (no VC required);

      =1, AL150 type;

      =2, AL200 type;

      =3, input VC file.

   2. NRANGE

      Number of wavelength ranges.

   3. WMIN WMAX IORD Q(0) ... Q(IORD)

      (NRANGE of these cards are given).

      WMIN, WMAX: minimum and maximum lambda values (in Angstroms) for this range;

      IORD: order of the polynomial;

      Q(0) ... Q(IORD): polynomial coefficients determined by single reflections.

   4. IMAX

      Spots with intensities > IMAX to be rejected.

   5. IMIN

      Spots with intensities < IMIN to be rejected.

   6. SIGREJ

      Spots with I < SIGREJ*SIGMA(I) to be rejected.

   7. INT_TYPE

      Intensities from box integration (1) or profile fitting (2)

   8. NLOG

      Number of spots to be written in .log file.

   9. CLASS

      =2, 3 ..., doubles, triples ... to be deconvoluted;

      =all, all mutiples to be deconvolted.

   10. SCALE

       Output intensities to be mutiplied by SCALE.

5. Control file for LAUENORM

   See the LAUENORM documentation.

6. The Laue .ge1/.ge2 data files

7. The singles reflection file (.mtz)

8. The Victoreen coefficients file (for film only)

The output files are as follows:

1. Multiples reflection file: .mtz

2. Combined (singles + multiples) reflections file: .mtz

RUNNING THE PROGRAMS

Use the command 'laue deconv'

The deconv.com command file will be created after the first run. The iteration can be performed using 'laue deconv.com'. If any .mtz file is to be used as a starting point in the current run, the file name after 'fftbig hklin' in deconv.com should be replaced by this .mtz file.

REFERENCES

1. Collaborative Computational Project No. 4 (1994) Acta Cryst. D50 760-763

2. Hao Q., Campbell J.W., Harding M.M. and Helliwell J.R. "Evaluation of Reflection Intensities for the Components of Multiple Laue Diffraction Spots by Direct Methods" Acta Cryst. (1993) A49 528-531

3. Hao Q., Harding M.M. and Campbell J.W. "Evaluation of Reflection Intensities for the Components of Multiple Laue Diffraction Spots. III. using a Real-Space Density Modification Method" J. Synch. Rad. (1995) 2 27-30

EXAMPLES

fft.ctl

TITLE 4Zn Insulin (SPG R3) Patterson map
LABIN F1=F
SCALE F1 0.01156 0
VF000 0 76632
PATTERSON
GRID 108 108 54
AXIS Y X Z
XYZLIM 0 107 0 107 0 17

MOD MAP
0. 2 1000

TITLE Fc's for 4-Zn insulin
MODE SFCALC MAPIN HKLIN
GRID 108 108 54
RESO 100. 2.298
NOSCAL
LABIN FP=F SIGFP=SIGF
LABOUT FC=FC PHIC=PHIC
END

3
2
.495 .905 4 170.87266 -856.44730 1634.9119 -1397.6714 449.50245
.92 1.6 4 38.897889 -121.49140 144.85515 -77.188736 15.478087
9000
100
5
2
0
all
100.

ZN1.AFOUT and ZN2.AFOUT from DECONV
80.7 80.7 37.6 90 90 120
SCALE 2
INPUT
INPUT
1 0.5014
0 -5.637
146 2 1 0 5 0 1
1 1 2000 0.0 0 0 0 0.0
.495 .905 6 4 0 4 170.87266 -856.44730 1634.9119 -1397.6714 449.50245
.93 1.6 6 4 1 4 38.897889 -121.49140 144.85515 -77.188736 15.478087
1