DetDirax

Programs

• pk2drx
  This program reads a pk file and writes c-vectors to a drx file.
• dirax
  Reads a drx file, and tries to find the best cell parameters.

Files

• dirax.init
  If a file dirax.init does not exist, it will be created. This file is used for every DirAx run. You have to supply the following information

  Name	default	description
  dmax	150	maximum expected axis length
  maxtrio	30000	maximum number of triplets
  volmin	0.3*dmax**3	minimum expected volume
  volmax	2.0*dmax**3	minimum expected volume

  Possible cells are only accepted if the cell volume lies between volmin and volmax. With a large number of reflections you could increase maxtrio.
  You can always edit dirax.init at a later stage.
• pk file
  You will need a pk file. This file can be created with the peak search commands in view. The following data from the pk file are essential:

  Name	description
  DETZERO	the detector offsets
  IMPACT	impact data (hor and ver)
  IMPACT3	impact data (hor, ver and rot)

Start

• The program starts by running pk2drx on the supplied pk file to check if the pk file is useable.
• If non-zero detector offsets are found in the pkfile, you are asked to do the search relative to these offsets.
• code
  Enter the name for this run. All intermediate results will be stored in directories 'code'_P* and 'code_N*. If these directories already exist, you are asked to load the rmat files from these directories.
• Grid size
  The determination of the detector offsets is done using a 3-dimensional grid search. The grid runs from -21 to +21 for distance, and from -141 to 141 for both horizontal and vertical in all 3 directions. The default grid size is 0.1 mm.
• With Graphics?
  Answer yes if you want to monitor the progress of the procedure.

Strategy

1. menu
   Setup a single gridsearch.
2. fast
   Setup a single gridsearch. When done, the stepsize in each direction will be halved until all steps equal the grid size. A new gridsearch will be setup around the best position of the previous search.
3. auto
   Setup a single gridsearch. When done, the stepsize in each direction will be halved and the number of steps will be doubled and the process will be repeated until the whole grid has been evaluated.
4. permutations
   Use this option if detector offsets are available but their definition is unknown The program will setup a grid with all 8 possibilities.

• Central position
  Specify the position in mm.
• Number of steps in each direction
  
• Stepsize in each direction
  Specify the stepsize in mm. The program will use a stepsize in grid units.

Examples

• Example 1
  several crystals with tetragonal symmetry (a=60, c=320)

detdirax Commands

again

auto

central

correct

• none
  No correction will be applied
• normal
  Commands and options will be corrected.
• full
  As before plus possible corrections are printed
• debug
  As before plus all available commands/options are printed

delta

diraxoption

• randomize
  dirax will use up to 1000 reflections. If more are supplied, a random slection will be taken. dirax builds a list of triplets using a random generator. By invoking randomize, these selections will be different for different runs of dirax. This can be usefull if some dirax runs fail to give a solution. See again.
• go
  Start the dirax process. Possible solutions will be filtered with the settings from the file dirax.init. Select the best solution.
• go
  Another run, but now starting with the fitting reflections of the best solution of the previous go. Sometimes this will improve the best cell, sometimes you will loose a possible solution

exit

fast

fom

• nfit
  

     nFit  = number of fitting reflections
     nRef  = total number of reflections
     Fom   = 100*nFit/nRef

• volume
  

     CellRadius    = CellVolume^(1/3)
     CellRadiusMax = CellVolume^(1/3) for the largest CellVolume
     nFit          = number of fitting reflections
     nRef          = total number of reflections
     Fom           = 100 * CellRadiusMax/CellRadius * nFit/nRef

• distance
  

     f                  = DetectorDistance + nstep(1)*delta(1)
     DistanceCorrection = (DetectorDistance/f)^(1/3)
     Fom                = DistanceCorrection*FomVolume

  
  Only useful if multiple distances are used (delta(1)>0 nstep(1)>1)

go

• Draw a yellow box for the gridpoint
• The program pk2drx will be run to create a new drxfile, using the standard pkfile and the offsets corresponding to the current gridpoint.
• Run dirax of the new drxfile, and find possible cells (using diraxoptions). Finally, an rmatfile will be created
• Read the rmatfile, and extract the cell volume and number of fitting reflections.
• Calculate a Figure Of Merit (see fom)
• update the graphics

grid

load

menu

nstep

output

permutations

pick

picksave

• create name.rmat
• create name.pec. This file can be used to load the results into peakref. It sets an appropriate value for maxmismm, reads the rmatfile and pkfile, initialises the values for detzero and reindexes the reflections.
• create name.drx

plot

printtodo

save

• create name.rmat
• create name.pec. This file can be used to load the results into peakref. It sets an appropriate value for maxmismm, reads the rmatfile and pkfile, initialises the values for detzero and reindexes the reflections.
• create name.drx

show

size

status

windowlog