[phenixbb] mr_rosetta: how to continue from recovered mr_protocols.default run

Terwilliger, Thomas C terwilliger at lanl.gov
Tue May 21 07:34:54 PDT 2013

Hi Christian,

Yes, this is a bit of a problem. As you figured out, you can restart mr_rosetta after a completed stage such as rosetta_rebuild, but not from the middle of a stage.  If you complete a stage manually (as you did) there is no solutions.pkl file to tell mr_rosetta what has been done, so it is not able to go on from there.

Instead, what you might try (if feasible in your case) is choose the best rosetta model or models (based on scores). Then put those together to make a new complex...and then start all over with that as your new model (with already_placed=True), or put it into autobuild and then recycle it in mr_rosetta.  This is more or less what mr_rosetta was going to do.

Let me know if that doesn't work,
All the best,
Tom T

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Christian Becke [christian.becke at fu-berlin.de]
Sent: Tuesday, May 21, 2013 6:36 AM
To: phenixbb at phenix-online.org
Subject: [phenixbb] mr_rosetta: how to continue from recovered  mr_protocols.default run


I am trying mr_rosetta on a complex. At the GROUP_OF_ROSETTA_REBUILD
stage, my machine ran out of memory and the mr_protocols.default
processes were killed. After adding more swap space, I restarted the
mr_protocols.default runs (3 parallel jobs, one for each chain) using
the scripts RUN_?/WORK_?/run_rebuild.sh, which appear to have finished
correctly (i.e., there are 20 pdb files generated for each of the chains).
However, I could not figure out how to restart mr_rosetta so that it
picks up these models. Any suggestions?


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