Applications

The areas of application of ARP/wARP Version 5.0 include:

1.

Refinement of MR solutions
If the initial model (a Molecular Replacement solution) needs to be substantially improved then unrestrained xyzB reciprocal space refinement may be carried out with ARP/wARP performing updating of the whole model. Resolution of the data should be 2.0 Å or higher. The output is a set of ARP atoms (the ARP model). The ( $3F_o-2F_c / 2mF_o-DF_c, \alpha_c$) map should be calculated from the ARP model and analysed carefully (yes, it's graphics time). The initial or the ARP model is then rebuilt to fit this map. Very often, if the X-ray resolution is high enough and the initial model is not completely wrong, the ARP atoms are located at approximately the true protein atom positions even in the case of unrestrained refinement. So they can be quite happily used as guides for rebuilding.

Please note, that for difficult cases approaches such as described for application #4 might work better even when starting from a molecular replacement solution.

2.

Improvement of MIR(AS) phases
ARP/wARP can be used to build a protein-like model consisting of a set of non-connected atoms (free atoms model) into a MIR map. This model is then refined as described above for #1.

3.

Averaging of multiple refinements
ARP/wARP can be used to prepare models and command scripts for several independent refinement runs as described for #1 and #2. 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. The ( $F_o, \alpha_{\rm wARP}, FOM_{\rm wARP}$) map is then calculated and should be inspected. Resolution of the data should be 2.3 Å or higher.

4.

Automatic tracing of the density map and model building
THIS IS NOT YET PART OF THE PRESENT SOURCE DISTRIBUTION. The $\alpha$-version is available as an Irix executable.

This application mode takes as input a map or a model (for example the output of one of the ARP/wARP scripts) or in favourable cases directly an experimental map and delivers an essentially complete model (the success is obviously strongly dependent on the map quality).

Combined with refinement as described for #1, #2 or #3, it significantly enhances the procedure. Resolution of the data should be 2.3 Å or higher. The output is a set of regularised polypeptide fragments, which are then used as an initial model for restrained refinement with ARP/wARP , further automatic tracing, more refinement, etc. in an automated manner.

5.

Building of the solvent structure
If the initial model is more or less correct, i.e. an R factor of about 30 % or less, 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 close 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.

6.

Ab initio structure determination for metalloproteins
ARP/wARP was successfully applied to the small, 52 amino acid protein rubredoxin. This structure could be solved ab initio. The success was clearly due to the the presence of the FeS₄ cluster in the protein. The positions as derived from the Patterson synthesis were used as a starting model. This initial model gave an R factor of 53% at 0.92 Å resolution. The resulting ARP model gave an R factor of 16% and map correlation to the final model map of 90%. Subsequently the successful solution was obtained with X-ray data truncated to 1.6 Å.