Major changes in version 6.0

• ARP/wARP 6.0 offers a full graphical user interface based on the CCP4i GUI. This is intended to hide the automated scripts of the previous version. The use of the ARP/wARP module within the CCP4 interface is straightforward and self-explanatory. The scripts are still fully functional but their use to drive the packages routines is no longer supported.
• The standard refinement engine in now REFMAC 5 from the CCP4 software suite although the previous version is also supported.
• The main chain tracing routines have been superseeded by an introduction of a pattern recognition of an electron density map and a novel algorithm based on a depth first graph search strategy. The tracing module is now able to trace structures at a resolution as low as 2.5 Å and it finds more peptide fragments compared to the previous algorithm, although it is somewhat slower. The previous algorithm was limited to around 2.0-2.3 Å but is still also provided within the suite. An iteration of the new tracing module with reciprocal space maximum likelihood refinement now converges 3 to 5 times faster compared to the Version 5.1
• The side chains routines are now based on a full probabilistic formalism. They are also available as a stand-alone module for real space refinement and rebuilding, called "guiSIDE". They can be used to rebuild from scratch all side chains of a molecule, even with 3.0 Å maps (but no autotracing). It is good to check the rebuilt model against your model in O and look for deviations. Side docking takes 1-2 minutes for a 500 residues protein, including real space torsional refinement. It only accepts the 20 standard aminoacids and does not yet work automatically with multimers. The side chain docking routine can now be used during autotracing cycles, thus obtaining in every building cycle a model with side chains refined in real space.