[phenixbb] AutoBuild runtime

Nathaniel Echols nechols at lbl.gov
Sat Nov 5 12:17:27 PDT 2011

On Sat, Nov 5, 2011 at 12:02 PM, Shya Biswas <shyabiswas at gmail.com> wrote:
> I was running autobuild using my protein sequence and the best MR model that
> I got out of phaser, however it is taking really long to finish the job. Is
> there a way to reduce the time period?

Several options:

- turn on quick mode (quick=True, or equivalent button in GUI)
- use multiple processors if you have them (nproc=X, or equivalent
control in GUI)
- cut back resolution: if you have really good and/or high-resolution
data*, you may be able to get nearly as good a model with fewer
reflections, and it will be much faster (mostly due to refinement
time, I think).  However, this can also significantly degrade your
model if the data aren't that great.
- instead of AutoBuild, use phenix.phase_and_build (also in the GUI),
which is basically the building procedure from AutoSol.  It will
usually not produce as complete a model (or R-factors as low) as
AutoBuild, but it's much faster.


(* the p9-sad tutorial is a good example of this - when we run
workshops, we usually tell attendees to set the resolution limit for
AutoSol to 3.0 instead of using all data to 1.7.  The resulting model
is nearly complete, and it finishes in less than half the time.  Of
course these data are unusually good...)

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