Crystallography Laboratory University of Nijmegen

CRUNCH

14. Examples

Converting a local structure factor file named 'xtal.dat'. In this example the user typed:
```
crunch hornef conhkl xtal.dat
```
The following information appeared on the screen - the bit in [ ] was provided by the user -:
```
=================================================

*** CONHKL  conversion of reflection files 
================================================= 

*** The first record on your reflection-file is: 

HKL    0   -2    0       66.23596        0.90171 1 SKIP 

==> You must now specify your record type using keywords 

*** Example: hkl skip fobs sigma 

*** This means: 

*** The first 3 numbers are h,k,l, the 4th should be skipped, 

*** the next one is Fobs and the last one is sigma(Fobs) 

*** Typing f2obs instead of fobs tells the program your file 

*** contains F**2 rather than F 

==> Specify your record: [skip hkl fobs sigma skip] 

=================================================

STOP Ready, normal end statement executed 

*** conhkl ended 

================================================= 
```
Users of the package XTAL will recognize the record shown as typical input of ADDREF, the program in XTAL which reads in structure factors. Hornef is the name of the compound. The programs shows the first record of the file, followed by an explanation on how to proceed. Here the records consist of a bit of text, h,k,l, Fobs, sigma(Fobs) and some other information which Crunch does not need. By typing the record between brackets the user tells Crunch to skip the first item and to consider the next five numbers as h,k,l, Fobs and sigma respectively. The rest of the record is skipped again. Use lower case characters here! At the end of the run the file 'hornef.frefa' was prepared, ready for use by Crunch and Dirdif.
Trying to solve a structure the first time. The user next typed
```
crunch hornef try
```
On the screen appeared:
```
Crunch interactive, always give return to choose defaults 

CELLCO C 92 H 72 O 20 

The structure is an Equal_atom structure 

[D]efault or [U]ser specified matrix construction? 
```
The cell contents are shown on screen. Crunch has decided that hornef is an equal atom structure. The user gave a return on the next question as he wanted to try a default run of Crunch. In this case a maximum of 10 random starting sets is tried. If you next run Crunch you will not be asked these questions again. Should you want to change anything, for instance the way the Karle-Hauptman matrices are constructed, you will have to remove the file 'code.par', in this case hornef.par. You may choose to use the command 'crunch code clear' instead.
The user wants to collect the results of a number of trials, to see whether there are any (non)solutions which look more promising than the others. See the section 'What to do inthe case of problems?'. She typed:
```
crunch hornef collect 1 25
```
After a few moments the unix prompt reappears.
On completion the file 'hits' is inspected. Solution number 9 looks better than the others: A higher value of the determinant and a lower final value of R2 are the criteria to look for. The user now typed:
```
crunch hornef recycle 9 15
```
Again after a few seconds the unix prompt reappears. Crunch will do the calculation for trial number 9 again. However, instead of proceeding to trial 10 in the case of failure, the best model obtained is used to calculate phases which are used as starting values for the maximization of the determinants. The refined phases are used to calculate a new start for the second section of Crunch. In this case this is done six times (15-9). Of course Crunch stops iterating if a satisfactory solution is obtained. Note that it is not necessary to use the options 'try' or 'collect' before using quot;recycle'. It is perfectly valid to try to solve your structure using a run such as:
```
crunch hornef recycle 1 10
```

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Crystallography Laboratory University of Nijmegen

CRUNCH

14. Examples

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