Error in loop modeling protocol

[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>

[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>

[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?

[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 *

[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.

[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

[Author]

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