[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
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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