[phenixbb] STOPWIZARD

Thomas C. Terwilliger terwilliger at lanl.gov
Mon Oct 17 12:53:58 PDT 2011

Hi Morten,

Yes, you can use STOPWIZARD to stop a phenix wizard, including mr_rosetta.
 However the "restarting" part is no longer enabled for most of the

For mr_rosetta, you can restart. Here is how:

You can re-start mr_rosetta only at the beginning of major stages (like
"place_model", "rosetta_rebuild" etc)...but not in between.

Normally at the end of a major stage a .pkl file is written out with text
like "type this to see all the results".  You can almost always give your
original command, the command "start_point=xxx" and
"mr_rosetta_solutions=my_pickle_file.pkl" and it should then continue on
from there.

I will put this in the docs...

All the best,
Tom T

>> Dear phenixbb,
>> The Phenix manual mentions several times that making a file named
>> in the wizard root directory will stop the wizard in an orderly fashion
>> the
>> next time it checks for STOPWIZARD. There is however no mention of how to
>> properly restart the wizard after having stopped it... How? I seem to
>> remember something about it being
>>>phenix.appropriate_wizard params_used_in_wizard.eff
>> but I'd like be sure that I don't simply start over by doing that.
>> Also can I then change the parameters before restarting the wizard? Say,
>> hypothetically of course, that I've started mr.rosetta and asked for 1000
>> prerefined models and realised that it will take ridiculously long and be
>> rather redundant since I specified both the .hhr file from global and
>> local
>> alignment and the top hit has two chains (resulting in mr.rosetta wanting
>> to
>> build 4000 prerefined models) but I don't want to throw away the 700
>> models
>> already built. Could I do something about that?
>> Sincerely,
>> Morten Grøftehauge, PhD
>> Durham University
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>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb

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