Hello all,

I have been trying (desperetly) to run the Rosetta_MR.

I have encountered some problems with my data, so I switched to the "HNP3-mr-rosetta" tutorial dataset.

I followd the debugging suggestions in the instructions webpage with no improvement. It seems that I have a problem in the rebuild stage.

Attached are the RUN_FILE_1.log from REBUILD_IN_SETS_5 and ../WORK_1/rebuild.log. The edited_align.ali file cannot be opened for some reason.

Another issue is that the map used is being taken from "overall_best_denmod_map_coeffs_nf.map" instead of "cycle_best" (as is in the tutorial's mr_rosetta_output log). this seems to produce an error (last log file attached).

What should I do next?

Thank you,

Yoni

Parameters taken from: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/PARAMS_1.eff

# mr_rosetta_rebuild

# Run automr mr_rosetta_rebuild with rosetta

# Type phenix.doc for help

Values of all params:

mr_rosetta_rebuild {

input_files {

model = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/1zmm_mr.1.pdb"

map = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoBuild_run_1_/overall_best_denmod_map_coeffs_nf.map"

seq_file = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/EDITED_1dfn.seq"

hhr_files = None

alignment_files = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/edited_align.ali"

model_info_file = ""

fragment_files = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/phaser_rosetta/aat000_09_05.200_v1_3.gz"

fragment_files = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/phaser_rosetta/aat000_03_05.200_v1_3.gz"

fragment_files_chain_list = None

fragment_files_9_mer_by_chain = None

fragment_files_3_mer_by_chain = None

use_dummy_fragment_files = False

sort_fragment_files = True

}

output_files {

log = "mr_rosetta_rebuild.log"

params_out = "mr_rosetta_rebuild_params.eff"

}

directories {

temp_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1"

workdir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1"

output_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1"

gui_output_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta"

top_output_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14"

rosetta_path = "/Users/administrator/rosetta_3.4"

rosetta_binary_dir = "rosetta_source/bin"

rosetta_binary_name = "mr_protocols.default.macosgccrelease"

rosetta_script_dir = "rosetta_source/src/apps/public/electron_density"

rosetta_pilot_script_dir = "rosetta_source/src/apps/pilot/frank/"

rosetta_database_dir = "rosetta_database"

}

rosetta_rebuild {

run_rosetta_rebuild = True

stage_to_rebuild = "rescored_mr_solution"

max_solutions_to_rebuild = 5

min_solutions_to_rebuild = 1

llg_percent_of_max_to_keep = 50

rosetta_models = 20

chunk_size = 1

edit_model = True

superpose_model = False

}

rosetta_modeling {

map_resolution = 3

map_grid_spacing = 1.5

map_weight = 1

map_window = 5

include_solvation_energy = True

weights_file = ""

}

crystal_info {

resolution = 0

space_group = "P 21 21 2"

chain_type = *PROTEIN DNA RNA

ncs_copies = 1

}

control {

verbose = False

debug = False

raise_sorry = False

dry_run = False

nproc = 1

group_run_command = "sh "

queue_commands = None

condor_universe = "vanilla"

add_double_quotes_in_condor = True

condor = None

one_subprocess_level = None

single_run_command = "sh "

last_process_is_local = True

background = True

ignore_errors_in_subprocess = True

check_run_command = False

max_wait_time = 100

wait_between_submit_time = 1

wizard_directory_number = 14

n_dir_max = 100000

number_to_print = 5

write_run_directory_to_file = "/Users/administrator/Yoni/Rosettal

tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/INFO_FILE_1"

resolve_command_list = None

start_point = place_model rescore_mr rosetta_rebuild rosetta_rescore \

similarity refine_top_models average_density_top_models \

relax_top_models autobuild_top_models \

setup_repeat_mr_rosetta repeat_mr_rosetta

stop_point = place_model rescore_mr rosetta_rebuild rosetta_rescore \

similarity refine_top_models average_density_top_models \

relax_top_models autobuild_top_models \

setup_repeat_mr_rosetta repeat_mr_rosetta

clean_up = False

}

non_user_params {

file_base = "1zmm_mr.1"

print_citations = False

highest_id = 10

is_sub_process = True

dummy_autobuild = False

dummy_refinement = False

dummy_rosetta = False

prerefine_only = False

skip_clash_guard = True

correct_special_position_tolerance = None

comparison_mtz = ""

labin_comparison_mtz = None

write_local_files = False

rosetta_fixed_seed = None

}

Starting mr_rosetta_rebuild

Date: Thu Dec 20 14:44:49 2012

Directory: /Users/administrator/Yoni/Rosettal tutorial

data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5

HOST = ZagottasMacPro.local

HOSTTYPE = intel-mac

MACHTYPE = x86_64

OSTYPE = darwin

VENDOR = apple

USER = administrator

PID = 36828

Checking rosetta paths:

rosetta binary:

/Users/administrator/rosetta_3.4/rosetta_source/bin/mr_protocols.default.macosgccrelease

database_dir: /Users/administrator/rosetta_3.4/rosetta_database

script_dir: /Users/administrator/rosetta_3.4/rosetta_source/src/apps/public/electron_density

pilot_script_dir:

/Users/administrator/rosetta_3.4/rosetta_source/src/apps/pilot/frank/

Changing to work directory: /Users/administrator/Yoni/Rosettal

tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1

Rebuilding the model /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/1zmm_mr.1.pdb

with rosetta

Rebuilding model using map at resolution of 3.0 A

Generating 20 rebuilt models

================================================================================

Reading model from /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/1zmm_mr.1.pdb

================================================================================

ALIGNMENT LINES:

## TARGET 1zmm_

# hhsearch

scores_from_program: 0 1.00

0 DCYCRIPACIAGERRYGTCIYQGRLWAFCC

1 -CYCRIPACIAGERRYGTCIYQGRLWAFCC

Trying to adjust the PDB sequence from alignment file:

-CYCRIPACIAGERRYGTCIYQGRLWAFCC

to match the actual PDB sequence:

YCRIPACIAGERRYGTCIYQGRLWAFCC

New alignment line 4 for PDB:

1 --YCRIPACIAGERRYGTCIYQGRLWAFCC

Start position of target sequence in sequence file: 0

Aligned model for comparison: /Users/administrator/Yoni/Rosettal

tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1/WORK_1/aligned_model.pdb

Log for rebuilding: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1/WORK_1/rebuild.log

**************ERROR ENDING********************** Failed to run REBUILD...see log file in /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1/WORK_1/rebuild.log

**************ERROR ENDING**********************

---

Here is ../WORK_1/rebuild.log:

core.init: Mini-Rosetta version unknown from unknown

core.init: command:

/Users/administrator/rosetta_3.4/rosetta_source/bin/mr_protocols.default.macosgccrelease

@rebuild.flags

core.init: 'RNG device' seed mode, using '/dev/urandom',

seed=345021854 seed_offset=0 real_seed=345021854

core.init.random: RandomGenerator:init: Normal mode, seed=345021854

RG_type=mt19937

ERROR: Warning: can't open file /Users/administrator/Yoni/Rosettal/

tutorial/ data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/edited_align.ali!

ERROR:: Exit from: src/core/sequence/util.cc line: 380

---

core.init: Mini-Rosetta version exported from unknown

core.init: command:

/Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_source/bin/mr_protocols.default.macosgccrelease

@rebuild.flags

core.init: 'RNG device' seed mode, using '/dev/urandom',

seed=-340184367 seed_offset=0 real_seed=-340184367

core.init.random: RandomGenerator:init: Normal mode, seed=-340184367

RG_type=mt19937

core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard

core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12

core.scoring.etable: Starting energy table calculation

core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well

core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)

core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)

core.scoring.etable: Finished calculating energy tables.