Crystallography Laboratory University of Nijmegen

The questions:

• What is Crunch?
• Why the name Crunch?
• Is Crunch designed for equal atom structures or not?
• Is the installation of Crunch difficult?
• During compilation I get warnings. Is this bad?
• Is there or will there ever be an MS-DOS version?
• When I install the program suite and run it the first time on the test structure nothing happens. What did I do wrong?
• I don't understand the differences between the try, collect and recycle commands
• What is the largest number of reflections I can put into the program?

Question:

What is Crunch?

Answer:

Crunch is a system of Fortran programs and Unix shell-scripts. The aim is the automatic solution of the phase problem in single crystal X-ray diffraction. Given the measured intensities and the usual data such as contents and dimensions of the unitcell, in general Crunch will successfully determine your crystal structure for you.

Question:

Why the name Crunch?

Answer:

This is not an acronym based on something like Comprehensive Retrieval of Unlikely Natural Compounds' History but rather a vivid description of the effect of the software on the phase problem.

Question:

Is Crunch designed for equal atom structures or not?

Answer:

Crunch is designed for solving the phaseproblem in difficult small to medium sized equal atom structures (N<200). However, the system may be used for heavy atom compounds as well. The method is a multi-solution one, the number of trials needed for a simple case is usually very small (< 5).

Question:

Is the installation of Crunch difficult?

Answer:

Installation is automatic. You just need to answer one or two questions regarding your local setup. Follow the instructions given in the Howto file. Note the current version (1.0) no longer requires the presence of the Dirdif program suite on the computer you'd like to use Crunch on.

Question:

During compilation I get warnings. Is this bad?

Answer:

Yes, this means I've been a bit sloppy here and there. However, I have not met with any problems due to these inaccuracies. Not yet anyway. I aim to clean up the software before posting the next version.

Question:

Is there or will there ever be an MS-DOS version?

Answer:

The limitations of Dos and the amount of work involved in maintaining a system like Crunch for different operating systems have forced me to limit my support to one operating system only: Unix. As you may have noticed I do support different platforms, including Linux on the PC.

Question:

When I install the program suite and run it the first time on the test structure nothing happens. What did I do wrong?

Answer:

Probably everything went perfectly well. Default the Crunch procedure runs in the background. As a result no messages appear on the screen while the program is running. Also, on modern fast computers solution of the test structure is so rapid that Crunch may be finished before you had time to type "ps". Check the nohup.out file, the hits file and the ccode.report file.

Question:

I don't understand the difference between the try, collect and recycle commands.

Answer:

The option "try" will start the system until in a certain cycle the solution is found. It then stops and the resulting files will contain information corresponding to this solution. By default Crunch will try 10 times, if you want more or perhaps fewer trials specify the values for "start" and "end", according to the example given in the manual.

The option "collect" will start the system and go through all cycles you have specified. It will NOT stop when a solution is found. After this run you can pick the best solution by hand looking at the hits file. For actually getting this solution run the system again using the "try" option and specify the number of this specific cycle. For example, if you first gave the command "crunch ccode collect 1 100" and you feel cycle 67 might give you your structure, run the system again with "crunch ccode try 67 67". The files obtained will contain information on cycle 67.

With the "recycle" option you could also try to sort of "shake and bake" cycle 67 if this cycle yielded the best result but no direct solution. With the command "crunch ccode recycle 67 77" you select cycle 67 as the start of a recycling procedure with 10 cycles maximum.

Question:

What is the largest number of reflections I can put into the program?

Answer:

This depends on the amount of available RAM specified during installation. In principle, there is no limit as all memory allocations are dynamic within the RAM available to the program. However, certain compilers will not accept array dimensions above a particular limit.

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