Major changes in version 5.1

• The scripts for different tasks are now unified under a single script arp_warp.sh. This script also offers on-line help and optional command line parameter input.
• The side chain docking has been massively improved. It now builds all side chains for which the main chain fragment is assigned to sequence. Furthermore it chooses the best rotamer from a small torsion angle database and performs real space torsional refinement. It is also able to 'fill' small gaps between chains, up to 4 residues (this option has not been sufficiently tested yet). The side chain docking program can now be used during cycling, thus obtaining in every building cycle a model with side chains refined in real space. There is a slight chance of introducing bias here, since the 'correct' side chain will be 'forced' to density, so the maps should be inspected carefully afterwards. The same program can be used to 'mutate' a molecular replacement model to correspond to the 'new' sequence and side chains can be fitted before the start of refinement.
• Some annoying bugs are removed from 'reshuffle'. It can now handle up to 37,500 water molecules and more than 20 protein chains.
• Anisotropic scaling is added as a REFMAC option and is now default in all protocols.