Error in loop modeling protocol

This topic has 5 replies, 3 voices, and was last updated 11 years, 2 months ago by Anonymous.

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- October 18, 2013 at 2:08 pm #1732
  Anonymous
  I m trying to run the the given script loops.py its showing error
  
  Traceback (most recent call last):
  File “loops.py”, line 35, in
  ccd = CcdLoopClosureMover(my_loop, movemap)
  NameError: name ‘CcdLoopClosureMover’ is not defined
  
  Here is full log
  
  +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
  +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
  
  C:UsersZebrafishDesktopLOOPmodeingloop_modelingloop_modeling>python loops.
  py
  PYROSETTA_DATABASE environment variable was set to: C:Program Files (x86)PyRos
  ettarosetta_database… using it…
  PyRosetta 2.011 [r48543:49680M] retrieved from: https://svn.rosettacommons.org/s
  ource/trunk/rosetta/rosetta_source
  (C) Copyright Rosetta Commons Member Institutions.
  Created in JHU by Sergey Lyskov and PyRosetta Team.
  
  core.init: Mini-Rosetta version 48543:49680M from https://svn.rosettacommons.org
  /source/trunk/rosetta/rosetta_source
  core.init: command: app -database C:Program Files (x86)PyRosettarosetta_datab
  ase -ex1 -ex2aro
  core.init: NOTICE: rng device failure, using time as seed
  core.init: ‘Time’ seed mode, seed=1382105119 seed_offset=0 real_seed=-874350312
  core.init.random: RandomGenerator:init: Normal mode, seed=-874350312 RG_type=mt1
  9937
  PYROSETTA_DATABASE environment variable was set to: C:Program Files (x86)PyRos
  ettarosetta_database… using it…
  PyRosetta 2.011 [r48543:49680M] retrieved from: https://svn.rosettacommons.org/s
  ource/trunk/rosetta/rosetta_source
  (C) Copyright Rosetta Commons Member Institutions.
  Created in JHU by Sergey Lyskov and PyRosetta Team.
  
  core.init: Mini-Rosetta version 48543:49680M from https://svn.rosettacommons.org
  /source/trunk/rosetta/rosetta_source
  core.init: command: app -database C:Program Files (x86)PyRosettarosetta_datab
  ase -ex1 -ex2aro
  core.init: NOTICE: rng device failure, using time as seed
  core.init: ‘Time’ seed mode, seed=1382105119 seed_offset=0 real_seed=-874350312
  core.init.random: RandomGenerator:init: Normal mode, seed=-874350312 RG_type=mt1
  9937
  core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set
  . Created 6225 residue types
  core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue L
  EU_p:CtermProteinFull 116
  core.pack.task: Packer task: initialize from command line()
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotentia
  l/env_log.txt
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotentia
  l/cbeta_den.txt
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotentia
  l/pair_log.txt
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotentia
  l/cenpack_log.txt
  core.scoring.etable: Starting energy table calculation
  core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy w
  ell
  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.
  basic.io.database: Database file opened: scoring/score_functions/PairEPotential/
  pdb_pair_stats_fine
  basic.io.database: Database file opened: scoring/score_functions/hbonds/standard
  _params/HBPoly1D.csv
  basic.io.database: Database file opened: scoring/score_functions/hbonds/standard
  _params/HBFadeIntervals.csv
  basic.io.database: Database file opened: scoring/score_functions/hbonds/standard
  _params/HBEval.csv
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotentia
  l/env_log.txt
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotentia
  l/cbeta_den.txt
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotentia
  l/pair_log.txt
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotentia
  l/cenpack_log.txt
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotentia
  l/env_log.txt
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotentia
  l/cbeta_den.txt
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotentia
  l/pair_log.txt
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotentia
  l/cenpack_log.txt
  basic.io.database: Database file opened: scoring/score_functions/MembranePotenti
  al/CEN6_mem_env_log.txt
  basic.io.database: Database file opened: scoring/score_functions/MembranePotenti
  al/CEN10_mem_env_log.txt
  basic.io.database: Database file opened: scoring/score_functions/MembranePotenti
  al/memcbeta_den.txt
  basic.io.database: Database file opened: scoring/score_functions/MembranePotenti
  al/mem_pair_log.txt
  basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
  basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
  basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp
  
  basic.io.database: Database file opened: scoringscore_functionsramaRama_smoot
  h_dyn.dat_ss_6.4
  LOOP 77 85 81 0 0
  protocols.loops.loops_main: Pose fold tree FOLD_TREE EDGE 1 75 -1 EDGE 75 81 –
  1 EDGE 75 87 1 EDGE 87 82 -1 EDGE 87 116 -1
  protocols.loops.loops_main:
  FOLD_TREE EDGE 1 75 -1 EDGE 75 81 -1 EDGE 75 87 1 EDGE 87 82 -1 EDGE 87 116
  -1
  
  setting up movers
  core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments fr
  om file test_in.frag3
  Traceback (most recent call last):
  File “loops.py”, line 35, in
  ccd = CcdLoopClosureMover(my_loop, movemap)
  NameError: name ‘CcdLoopClosureMover’ is not defined
  
  C:UsersZebrafishDesktopLOOPmodeingloop_modelingloop_modeling>
- October 20, 2013 at 12:18 pm #9435
  Anonymous
  Error in loop modeling protocol its showing error “NameError: name ‘ccd_closure’ is not defined”
  
  log+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++log
  
  setting up movers
  core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments fr
  om file test_in.frag3
  core.chemical.ResidueTypeSet: Finished initializing centroid residue type set.
  Created 1980 residue types
  set up job distributor
  randomizing loop
  low res loop modeling
  Traceback (most recent call last):
  File “loops.py”, line 89, in
  ccd_closure.apply(p)
  
  NameError: name ‘ccd_closure’ is not defined
  
  C:UsersZebrafishDesktopLOOPmodeingloop_modelingloop_modeling>
- October 20, 2013 at 3:04 pm #9436
  Anonymous
  It looks like you need to change the line ccd_closure.apply(p) to ccd(p) from your first statement.
  
  Which version of PyRosetta are you using? Which test scripts are you using? Is this your own script or one distributed?
- October 22, 2013 at 3:01 pm #9434
  Anonymous
  Have you imported the appropriate library?
  
  If not, try adding this line to the top of your script:
  
  from rosetta.protocols.loops.loop_closure.ccd import *
- October 22, 2013 at 6:48 am #9437
  Anonymous
  i m using the current release “PyRosetta v2.012” it stuck again now the error is given bellow the “loops.py” script which i m using have been attached with this post this script is provided on line its not my own script: thanks
  
  Error Log++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++Error Log
  
  core.chemical.ResidueTypeSet: Finished initializing centroid residue type set.
  Created 1980 residue types
  set up job distributor
  randomizing loop
  low res loop modeling
  Traceback (most recent call last):
  File “loops.py”, line 89, in
  ccd(p)
  TypeError: ‘CcdLoopClosureMover’ object is not callable
  
  C:UsersZebrafishDesktopLOOPmodeingloop_modelingloop_modeling>python loops.
- October 22, 2013 at 2:39 pm #9440
  Anonymous
  Ok, thanks.
  
  I don’t know where you got the script, but please use either this demo, located on pyrosetta.org: http://graylab.jhu.edu/pyrosetta/downloads/scripts/demos/D080_Loop_modeling.py Or the test that is released with the PyRosetta binaries. These are maintained and tested with each release, so they should work ok.
  
  BTW, that line needs to change from ccd(p) to ccd.apply(p) as it is a mover. Movers work by accepting and changing a pose in their apply function. If you want to learn more, movers should be covered pretty early on in the tutorials.
  
  -Jared
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