[phenixbb] Wishful thinking with AutoBuild?

Thomas C. Terwilliger terwilliger at lanl.gov
Mon Aug 4 11:03:40 PDT 2008

Hi Francis,

I would say that a standard run of autobuild needs a decent map (after
density modification) where you can see where a model would be built.

If you have a worse map than that, or low resolution (>3.5 A), then try
this keyword:


in which case autobuild will run a lot faster and just try to build
secondary structure in, skipping all the loops and skipping chain
extension.  It can build helices where you can hardly see them. If you are
lucky then the map will get better after this..then you can try feeding
the resulting overall_best_denmod_map_coeffs.mtz and overall_best.pdb in
to a regular run of autobuild.

Best of luck,
-Tom T

> Hello all
> Given a mediocre to bad experimental density map, what hopes does
> AutoBuild have of building a model? i.e. Should I be able to tell
> clear helicies and side chain density in the experimental density map
> before even attempting an autobuild?
> Thanks
> FR
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
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> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
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