SHARP/autoSHARP Tutorials	previous
Chapter 3

What to do after an autoSHARP run

(if it didn't automatically build everything ... or even if it did)

Most of this has already been described in Chapter 1 - Fine-tuning. But some remarks might be helpful nevertheless.

A major stumbling block is the heavy atom detection. Experience shows, that higher wquality data seems to be necessary for detection heavy atom sites than is required for successfully phasing a project (once these sites have been obtained). Therefore, some more drastic data analysis (resulting in stricter resolution cuts or exclusion of dubious datasets) can help finding the sites.
Once a set of trustworthy sites has been found, the full scope of data and datasets can be used for the refinement and phasing (although this should still be 'real' data and not just a collection of Miller indices - so an honest approach towards criteria like I/sig(I) and completeness is advisable).
If no heavy atoms can be found within the current version of autoSHARP, one of the other, excellent external packages for doing this can be used (e.g. SHELXD, Shake-n-Bake, Hyss ...). The specification of a set of known sites in fractional coordinates or as a PDB file should make the transfer of sites found by an external program relatively straightforward.
autoSHARP tries to do a lot of data analysis at the beginning. And it tries to comment and present the results of this analysis in a meaningful fashion. Please take some time to go through these steps (especially if you are new to our autoSHARP or it is the first time you use a specific dataset). Notes should be checked and Warning messages corrected (if possible).
Although the automated analysis of residual maps tries to cover the most common scenarios (wrong sites or missed sites), a visual inspection is the only way to fully understand what is going on. Although it is possible to create these maps outside of our interface (these are simple MTZ files after all), it is much easier to use the tools we provide: so try and setup your browser and our helpers script correctly. This will allow you to quickly view maps, sites, bones and models e.g. in O or Xfit.
And if things get just slightly too complicated and tedious, noone wants to actually do them ... but there is no substitute for looking at residual maps. And no excuse for not looking at them will be accepted!
The density modification step leaves a lot of room for fine-tuning some of the parameters. The autoSHARP log file provides a direct link to the control panel specifically for these options. The explanation links on this control panel should give you some idea of what you could try.
The automatic building using ARP/wARP (as implemented in our program), is fine-tuned to the specific task (tracing from scratch in experimental density) and our phasing program SHARP. However, since the official ARP/wARP release allows more control over a variety of parameters, you might want to try using it instead the tools we provide.

Last modification: 16.11.04