[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 \
nproc=4
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
MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/rebuild.log
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,
Yonglin
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