[phenixbb] Questions about phenix.mr_rosseta

Yonglin Hu yonglinhu at gmail.com
Sun Feb 23 18:00:14 PST 2014

Hello List,

I am very new to using Phenix/Rosetta to solve MR. I just finished a job 
by following the procedures described on phenix-online.org using Phenix 
GUI. The program reported that no solution was found, but when I went 
through the RUN_FILE_*.log, I found that despite all the log files ended 
with the following sentences:

Stage to relax: refined_rescored_rosetta_solution
No solutions to relax
No autobuilt solutions to iterate...
Finishing up mr_rosetta...

one solution had a Rfree of 0.48 with correct number of molecules in 
ASU.  When I refined that solution using phenix, Rfree went down 
further, proving to be a correct one. So my question is: why 
phenix.mr_rosetta did not report this solution as a good one?

My second question is regarding model rebuild using phenix/rosetta. No 
matter I used the GUI or command lines copied from phenix-online like 
the following:

phenix.mr_rosetta \
   seq_file=~/MA/Mpa.pir \
   data=~/MA/MA.mtz \
   search_models=~/MA/refine_6.pdb \
   already_placed=True \
   fragment_files = ~/MA/MA-3mer \
   fragment_files = ~/MA/MA-9mer \
   rescore_mr.relax=False \
   rosetta_models=20 \
   ncs_copies=6 \
   space_group="C 1 2 1"  \
   use_all_plausible_sg=False \

the program always fails. The log files have the following messages:

Sorry, a subprocess has failed...
Sorry: Failed to run REBUILD...see log file in 

They pointed to rebuild.log files, but these files don't contain error 
message and they ended with the following seemingly innocuous lines:

protocols.relax.FastRelax: CMD: accept_to_best  -3682.86  0.994359 
0.994359  0.44
core.scoring.rms_util: WARNING: In CA_rmsd, residue range 1 to 402 
requested but only 401 protein CA atoms found.
core.scoring.rms_util: WARNING: In CA_rmsd, residue range 1 to 402 
requested but only 401 protein CA atoms found.
protocols.relax.FastRelax: CMD: endrepeat  -3682.86  0.994359 0.994359  0.44
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.jd2.JobDistributor: S_MA_R_0005 reported success in 4573 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 5 jobs considered, 5 jobs attempted in 
20716 seconds

I would appreciate it if you could tell me what could be the causes of 
the failures.

Thank in advance,


More information about the phenixbb mailing list