Crystallography Laboratory University of Nijmegen

9. Crunch syntax

You may use any one of the options given below running the program. Always type your alias or the name of the dynamic link to crunch.uni, followed by the complete specification of the run.

The general syntax of a Crunch commandline:

crunch code run [start end] [first n, last n, all]

Below the variables 'crunch' and 'code' have the following meaning throughout:

• crunch: The name suggested for the link to or the alias of crunch.uni
• code: Compound name (e.g. rn001 in the test structure).
• run: Defines the type of run which will be executed.
• start: The number of the first trial to be done.
• end: The number of the last attempt

The last two values must be specified if one of the options 'first' or 'last' is to be used

• conhkl filename

  This type of run has a syntax different from the others. Use this run to convert your local structure factor file into a crunch-friendly (.frefa) format. The filename should be given with extension(s). See for more information the section Examples.

• clear

  All files created by earlier runs of Crunch are removed. Only the .crysin, deter.use, autofour.use and .frefa files are kept.

• blessing

  E-values are calculated and saved for further use. The routines from the DREAR-suite, Levy and Eval are used. Reference: Blessing, R.H. & Smith, G.D. (1999). "Difference structure factor normalization for heavy-atom or anomalous scattering substructure determinations" J. Appl. Cryst. 32, 664-670. Until the option 'clear' is used to clean up, these E-values will be used rather than the ones calculated by Normal.

• try

  Crunch uses random starts from 'start' until a solution is found or 'end' is reached. If the structure is found various files such as code.pdb, code.spf and code.report are created. Some information on all trials done is present in the file 'hits'.

• collect

  Scan all crunch-attempts from 'start' to 'end'. The results are given in the file 'hits'.

• deter

  Only the section calculating the phases - Deter - is executed. The results are saved in files 'code.phi1...n'. As above, the calculations are done for the trials 'start' to 'end'.

• peaks

  The phases generated using the option 'deter' are converted into possible fragments, using exfft. This again is done for the trials 'start' through to 'end'.

• autofour

  This option may be used in two completely different ways:

  1. You may have found a heavy atom or a small part of the structure by using some other method. If you then prepare a .frefa file as was described above, followed by creating a file 'code.pek' containing the known part of your structure, you can try to extend the model to the complete structure by just typing 'crunch code autofour', not giving the values start and end. A description of the code.pek file is given below.
  2. You have created files 'code.pek1...n' by using the peaks option. Then type 'crunch code autofour start end' to try to extend one or more of the models obtained.
• recycle

  This option implements a sort of 'shake and bake' strategy. The trial 'start' is run in the normal way. If a solution is obtained then the program stops as usual. If not, the best model obtained in the Autofour section is used to calculate phases to be refined using Deter. A new model is found etc. This process is continued until the structure is solved or 'end-start+1' cycles are completed.

The values start and end are optional except if you are using 'recycle', 'deter' or 'peaks'. The default values are 1 and 10 respectively.

Using the option 'try', which is normal when you are trying to solve a structure, usually the second step, model extension using Autofour, is started with the largest consistent fragment present in the map. However, following the value of 'end' you may specify the options 'first' or 'last', followed by a number 'n', or 'all'. The effect is that the first 'n', the last 'n' or all peaks found in the map are used as input to Autofour. Remember to specify the values 'start' and 'end' if you'd like to use the options just described. The shell gets confused if you specify just the parameters 'first' or 'last', interpreting them as values for 'start' and 'end'.

An example run:

crunch rn001 collect 27 74 

crunch code try n n

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