A flowchart of the ARP/wARP procedure. The arrow on top indicates the flow of the data. ARP/wARP modules are labelled in the middle in grey shaded boxes; the numbers in parentheses refer to the steps in Procedure that describe them. The rounded rectangular boxes to the left represent input data (black for required data, light grey for optional input - the sequence - and medium grey for alternative input - the phases or a model) and to the right to the output data. The vertical span of the input / output boxes refers to the procedures they are connected to in the middle.

Model completeness achieved by ARP/wARP 7.0 ‘Classic’ as a function of resolution. The blue circles represent a set of diverse structures donated by users in http://xtal.nki.nl/Depot. For these the starting map and the final structure are both known and the model completeness is calculated as the percentage of correct residues compared to the residues in the final structure. The red circles represent a set of diverse structures submitted by users to the ARP/wARP web server (http://cluster.embl-hamburg.de/ARPwARP/remote-http.html). For these structures the starting map or model is known but no final structure is available; thus model completeness is calculated as the percentage of traced residues compared to the anticipated number of residues in the final structure as input by the user. A trend line (counting only the average top 50% of jobs) is also shown for these structures. The lower model completeness even at high resolution for the remotely submitted jobs compared to the Depot structures is likely due to the fact that very rarely all residues in a sequence can ever be built in a crystallographic structure and thus the ARP/wARP performance could be underestimated. We also cannot exclude that many cases that end up in our web server could be the ‘hopeless’ local cases that users attempt to run remotely after failure in their lab.

Trouble shooting for partially ordered ligands. (A) The difference electron density map in the area of the ligand. (B) The ligand adenosylmethionine as modeled in the deposited structure in the PDB (1v2x). (C) A full ligand as built with ARP/wARP. (D) A partial ligand (with the methionine moiety up to its C_β atom removed) built with ARP/wARP, which matches the density better.