[phenixbb] Confused by the output from Phenix autobuild jobs

Serah Wangari serah.wangari at gmail.com
Tue Nov 24 02:14:59 PST 2009

Dear Phenix users,

I have run a number of Autobuild jobs using the Phenix GUI and in all
cases, I'm not sure what output I should proceed with to the next

- The first job was for rebuilding a loop section in the model
(rebuild-in-place) - As far as I can remember, there was no mtz
generated from this job, I had to generate map coefficients with the
overall_best pdb and an old mtz using another refinement program. Did
I miss something during the job input step, so that no mtz was
generated, or how would I proceed in such a case?

- The next job involved rebuilding the whole model (rebuild-in-place)
- in this case, I took the overall_best pdb, but when I tried to open
the overall_best_refine_map_coeffs.mtz in coot, I got this error that
coot failed to find F/Phi columns in the mtz file. Then I checked in
the TEMPO directory, and I managed to open a random mtz from one of
the refinement cycles with coot, but I wasn't confident building into
that, so again I had to generate map coefficients using overall_best
pdb and an old mtz in another program.

- The other job was rebuilding (rebuild-in-place) another model with
composite maps generation - Here, in addition to the 12 mtz and pdb
files from the 12 omit regions, I got resolve_composite_map.mtz I
should assume as the only final output; and no final pdb. Again, this
mtz file doesn't have the F/Phi columns as I got the same error as
above in coot. I'm not sure how to proceed with this mtz......

I would really appreciate if someone could point me to the right
direction or at least direct me to some literature where the output
from Phenix autobuild jobs is explained - as I haven't come across
such info yet.

Thank you in advance,



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