Applications

The applications of ARP/wARP Version 5.1 include:

• Automated model building combined with refinement
  
  • Automatic interpretation of the density map and model building.
    This application, (warpNtrace) takes as input experimental or modified phases, a partially built model or a free atom model and is supposed to deliver an essentially complete model and obviously an improved map. Automated model building combined with refinement [6] turns out to be very powerful not only for delivering a complete model in most cases, but also offers further map improvement compared with other protocols. Resolution of the data should be at least 2.3 Å or higher. warpNtrace utilises the idea of the hybrid model in which protein and free atoms can co-exist. It keeps whatever was recognised as protein and the rest as free atom model and refines this hybrid model for a 'big' cycle, consisting of several (typically 10) ARP refinement cycles. Then it gets the latest map and tries to interpret it again and hopefully ends up with a better interpretation than the first one, makes a big cycle again, etc., etc. ... Please note that this is still considered an $\alpha$-version and only executables for the extra program modules are provided at present.
  • Model update combined with refinement.
    If the initial model from a molecular replacement solution or any other initial model needs to be substantially improved then xyzB reciprocal space refinement may be carried out with ARP/wARP  performing updating of the whole model but always using the remaining model as a source of restraints. Resolution of the data should be 2.5 Å or higher. However, we had some recent successes with 3.2 Å data, using a starting model which was only 60% of the total. The solvent content for this crystal was 75 %.
  • Free atoms refinement for improvement of M(S)AD and MIR(AS) phases.
    ARP/wARP can be used to build a protein-like model consisting of a set of non-connected atoms (free atom model) into a MIR map. This model is then refined. The resulting map is typically of better quality than the starting map and the refined free atoms model should be then used for the warpNtrace procedure. The more useful application of it is the multiple model averaging. In this case, ARP/wARP prepares models for several independent refinement runs as described above. The results are then processed in such a way that each reflection is given a weighted average phase, $\alpha_{\rm wARP}$, and a figure of merit, $FOM_{\rm wARP}$. The results, especially for modest resolution, are better compared to a single ARP/wARP refinement. Resolution of the data should be 2.3 Å or higher. This application remains very powerful for bad starting maps and when the resolution is very close to the 2.3 Å limit. In such cases, using that and then going to warpNtrace gives the best results.
• Building solvent structure
  If the initial model is more or less correct and essentially only the solvent needs to be improved, restrained (standard) reciprocal space refinement is carried out with ARP/wARP  performing automatic adjustment of the solvent structure. Resolution of the data should be 2.5 Å or higher. The output is the protein model with the solvent molecules transformed with symmetry operations to lie around the protein. The ( $3F_o-2F_c / 2mF_o-DF_c, \alpha_c$) and ( $F_o-F_c / 2mF_o-DF_c, \alpha_c$) maps should be inspected. For REFMAC and SHELXL command files for water building, see the examples/ directory.
• Ab initio structure determination for metalloproteins
  ARP/wARP was successfully applied to small metal containing structures: an 125 non-H aom Br-containing beta-cyclodextrin complex [4] and the 52 amino acid protein rubredoxin which contains an FeS₄ cluster. This structures could be solved ab initio. The success was clearly due to the the presence of the heavy atoms the positions which were derived from the Patterson synthesis and used as starting model. Subsequently the successful solution for rubredoxin was obtained with X-ray data truncated to 1.6 Å.