[phenixbb] phenix autobuild question

Partha Chakrabarti ppchak at gmail.com
Mon Sep 15 12:50:27 PDT 2008


Hi,
Is it the Dortmund Alex from AG EW? :)
Cheers, Partha


On Mon, Sep 15, 2008 at 7:11 PM, Alex Berndt <aberndt at mrc-lmb.cam.ac.uk> wrote:
> 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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> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>



-- 
MRC National Institute for Medical Research
Division of Molecular Structure
The Ridgeway, NW7 1AA, UK
Email: pchakra at nimr.mrc.ac.uk
Phone: + 44 208 816 2515



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