[phenixbb] phenix autobuild question

Alex Berndt aberndt at mrc-lmb.cam.ac.uk
Mon Sep 15 11:11:37 PDT 2008

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  

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,

Failed to carry out AutoBuild_multiple_models:
Sorry, subprocess failed...message is:
phenix.autobuild   \


Reading effective parameters from /someplace/home/someuser/work/ 

Sending output to  AutoBuild_run_1_/AutoBuild_run_1_1.log


Failed to carry out AutoBuild_build_cycle:




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

phone: +44 (0)1223 402113

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