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Crystallography Laboratory University of Nijmegen

CRUNCH

 

 


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:

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

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 
means crunch rn001 and collect "hits" from sets 27 to 74. Hits contains a brief report on this run. If you are using the option 'try' the results of the first successful run are summarized in a file code.report. Should you want to look at the results of a particular successful run collected in the file hits, use the command
crunch code try n n
Further examples may be found in the designated section.


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