[phenixbb] Confused by the output from Phenix autobuild jobs

Kendall Nettles knettles at scripps.edu
Tue Nov 24 05:55:13 PST 2009

Try open my rather than auto open mtz in coot and then look behind the main window for the dialog box to select phases

Kendall Nettles

On Nov 24, 2009, at 5:26 AM, "Serah Wangari" <serah.wangari at gmail.com<mailto:serah.wangari at gmail.com>> wrote:

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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