Automated Scripts

ARP/wARP is a command file driven package. This distribution has been complemented with a set of easy-to-use set-up scripts that we hope will help avoid mistakes and will generally improve the overall user-friendliness of the programs.
THE USER IS STRONGLY ADVISED TO RUN ARP/WARP USING THE AUTOMATED SCRIPTS PROVIDED WITHIN THE PACKAGE.
Of course, you may still generate your own command files - see the section on 'I hate automated scripts'. In fact, for the moment this might be a better choice for solvent building, especially towards the end of refinement where you might want to keep very good control of REFMAC parameters adjusting geometry weights, etc.
The current automated scripts are:

• arp_warp_setup.sh This is the basic script for setting everything up. Answering simple questions like which MTZ file, which labels to use, how many models, how many processors, etc. allows a general parameter file, warp.par, to be created which will be used for all subsequent jobs.
• arp_warp.sh This is the script to run all applications described in section 3.1.
• warp.sh This is the script for the multi model averaging application. It is invoked when you run arp_warp.sh mode warp in the case you asked for averaging of different models but can also be run directly if desired.
• warp_solve.sh This is the script for the ab initio structure solution application.
• side_dock.sh Takes a (partial) model autotraced with warpNtrace, docks the fragments into the protein sequence, build the side chains and does real space torsional refinement.
• shake.sh A simple but useful script that randomises the model and resets B factors of atoms for i.e. help escape local minima or after introducing a new free-Rfactor set.