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 use. 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" mailto:[email protected]> 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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