[phenixbb] phenix autobuild question

[aberndt at mrc-lmb.cam.ac.uk]

sorry, i just realised what EW meant, sorry, yeah, EW ;))
a

> 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
>> ---------------------------------------------------
>>
>> _______________________________________________
>> phenixbb mailing list
>> 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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>