[phenixbb] phenix autobuild question

Thomas C. Terwilliger terwilliger at lanl.gov
Mon Sep 15 11:52:50 PDT 2008

Hi Alex,

I'm sorry for both the failure and the lack of a clear message here!  I
will try to fix both.

Is this running phenix-1.3-final?  (If not, could you possibly run with
that version so we are on the same version.)

Can you possibly send me the end of the output in


which I hope will have an actual error message to look at?

The reason for the subdirectories is this: phenix.autobuild runs several
jobs in parallel (if you have set nproc ) or one after the other (if you
have not set nproc).  These subdirectories contain those jobs...which are
then combined together to give the final results in your overall
AutoBuild_run_1_/ directory.

I don't know the answer to the phenix.refine question...perhaps Pawel or
Ralf can answer that one.

All the best,
Tom T

> Dear phenix community,
> I started an AutoBuild run using the phenix GUI (ver 1.3 rc4) on a
> linux cluster. It worked okay and all the refinement looked pretty
> decent. However, after quite a while I obtained the following error
> message (see below). Would anyone please tell me what to do to prevent
> this error and get phenix get its job finished?
> Also, I don't understand why phenix AutoBuild creates 5 (or whatever
> number) AutoBuild_run_x in the AutoBuild-run_1/TEMP0 directory and not
> two dirs up in the tree. In other words in my /someplace/home/someuser/
> work/someproject/phenix2/AutoBuild_run_1_/TEMP0 directory are  more
> AutoBuild_run_x_ directories (with x=1 to 5). It is a bit confusing to
> me.
> A final question: I realised that the phenix.refine drastically
> increases the number of outliers. I know that thare is a weighting
> term someplace ... but what was it again?
> Many thanks in advance,
> Alex
> warnings
> Failed to carry out AutoBuild_multiple_models:
> Sorry, subprocess failed...message is:
> ********************************************************************************
> phenix.autobuild   \
> write_run_directory_to_file=/someplace/home/someuser/work/someproject/
> phenix2/AutoBuild_run_1_/TEMP0/INFO_FILE_1
> Reading effective parameters from /someplace/home/someuser/work/
> someproject/phenix2/AutoBuild_run_1_/TEMP0/PARAMS_1.eff
> Sending output to  AutoBuild_run_1_/AutoBuild_run_1_1.log
> ********************************************************************************
> Failed to carry out AutoBuild_build_cycle:
> failure
> ********************************************************************************
> ********************************************************************************
> work_pdb_file  "AutoBuild_run_1_/edited_pdb.pdb"
> working_directory  "/someplace/home/someuser/work/someproject/phenix2"
> worst_percent_res_rebuild  2.0
> ---------------------------------------------------
> Alex Berndt
> MRC-Laboratory of Molecular Biology
> Hills Road
> Cambridge, CB2 0QH
> U.K.
> phone: +44 (0)1223 402113
> ---------------------------------------------------
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