[phenixbb] Failed to carry out AutoBuild

Joao Renato Carvalho Muniz jrcmuniz at gmail.com
Tue Nov 11 09:24:48 PST 2008

Dear Phenix community,

I started an AutoBuild run using the Phenix GUI (ver 1.3 final) on linux.
However, I noticed 2 weird things: 1st, Phenix seems that can not
handle with alignment between the residues from pdb and sequence.seq,
flagging the "Rebuild in place not recommended as identity *
fraction_aligned is 0.0%" message but still trying to build the
structure with the option "include_input_model=False" I guess(?)...
and 2nd, after quite a while I obtained the following error message:

Failed to carry out AutoBuild_build_cycle:

child process stderr output:
  command: 'csh /someplace/somedir/somedir2/AutoBuild_run_2_/TEMP0/RUN_FILE_1'
File exists.

The alignment between MR.1.pdb and sequence.seq should be something like 80%+!

Also tried to run using the followed command line:

phenix.autobuild data=MR.1.mtz model=MR.1.pdb include_input_model=True
n_cycle_rebuild_max=5 seq_file=sequence.seq

Same problem as above.

Could anyone please tell me what to do to prevent this error and get
phenix get its job finished?

Many thanks in advance,


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