AUTO XPL: a Unix shell-script system to sequence X-PLOR refinement runs

A Unix shell script has been written to automate many of the individual computational steps involved in refining the crystal structure of a biopolymer using Axel Brünger's program X-PLOR. The script controls the sequential execution of different refinement operations, automatically piping the output from each operation into the input for the next operation. The performance of each individual operation is monitored in terms of the progression of the free R factor and the step is repeated with a smaller number of minimization cycles if necessary in order to achieve the lowest observed free R factor. Most refinement parameters can be adjusted or reset for each individual step, allowing long sequences of refinement operations to be executed without manual intervention. The script can also be used to automate the evaluation of the effect of variations in input-parameter values on the performance of a refinement procedure.