[phenixbb] Confused by the output from Phenix autobuild jobs

Thomas C. Terwilliger terwilliger at lanl.gov
Tue Nov 24 06:53:37 PST 2009

Hi Serah,

I think  Kendall's suggestion will solve 3 of your 4 problems. I will put
that in the documentation so that it will be more clear next time.

For #1, yes, you should get an mtz file for rebuilding loops with
rebuild_in_place. There should be a line near the end of your log file
that says somethine like:

---  Density-modified map coefficients FP PHIM FOM ---
hklout_denmod: AutoBuild_run_42_/cycle_best_2.mtz

and that is your map file. Let me know if that is not so.

On the other hand if you use phenix.fit_loops, there is no mtz created, as
you would supply an mtz for the procedure that would still be the mtz to

I hope that helps!
-Tom T

>> 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
>> step.
>> - 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,
>> Serah
>> --
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