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Rosetta CM round_thread.pdb doesn't exist and can't find pose (id = round)

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Rosetta CM round_thread.pdb doesn't exist and can't find pose (id = round)
#1

I'm trying to create a threaded model according to this tutorial: https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/RosettaCM

I'm not sure why I'm getting this error, how to debug it? 

[labusr@luxor rosetta_cm]$ ./rosettacm_setup.sh
ERROR:root:code for hash md5 was not found.
Traceback (most recent call last):
  File "/opt/UCSF/Chimera64-1.12/lib/python2.7/hashlib.py", line 147, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/opt/UCSF/Chimera64-1.12/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
    raise ValueError('unsupported hash type ' + name)
ValueError: unsupported hash type md5
ERROR:root:code for hash sha1 was not found.
Traceback (most recent call last):
  File "/opt/UCSF/Chimera64-1.12/lib/python2.7/hashlib.py", line 147, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/opt/UCSF/Chimera64-1.12/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
    raise ValueError('unsupported hash type ' + name)
ValueError: unsupported hash type sha1
ERROR:root:code for hash sha224 was not found.
Traceback (most recent call last):
  File "/opt/UCSF/Chimera64-1.12/lib/python2.7/hashlib.py", line 147, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/opt/UCSF/Chimera64-1.12/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
    raise ValueError('unsupported hash type ' + name)
ValueError: unsupported hash type sha224
ERROR:root:code for hash sha256 was not found.
Traceback (most recent call last):
  File "/opt/UCSF/Chimera64-1.12/lib/python2.7/hashlib.py", line 147, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/opt/UCSF/Chimera64-1.12/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
    raise ValueError('unsupported hash type ' + name)
ValueError: unsupported hash type sha256
ERROR:root:code for hash sha384 was not found.
Traceback (most recent call last):
  File "/opt/UCSF/Chimera64-1.12/lib/python2.7/hashlib.py", line 147, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/opt/UCSF/Chimera64-1.12/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
    raise ValueError('unsupported hash type ' + name)
ValueError: unsupported hash type sha384
ERROR:root:code for hash sha512 was not found.
Traceback (most recent call last):
  File "/opt/UCSF/Chimera64-1.12/lib/python2.7/hashlib.py", line 147, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/opt/UCSF/Chimera64-1.12/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
    raise ValueError('unsupported hash type ' + name)
ValueError: unsupported hash type sha512
Using rosetta from /home/labusr/rosetta/main/source/bin
Switching to directory: /tmp/tmpuGwc3p
Running /home/labusr/rosetta/main/source/bin/partial_thread.default.linuxgccrelease -database /home/labusr/rosetta/main/database -mute all -in:file:fasta /home/labusr/Desktop/chlamy_paper/denovo_prediction/alpha_tubulin/rosetta_cm/round12.fasta -in:file:alignment /tmp/tmpuGwc3p/converted_alignment.aln -in:file:template_pdb  /home/labusr/Desktop/chlamy_paper/denovo_prediction/alpha_tubulin/rosetta_cm/alpha_tubulin_round_12.pdb -ignore_unrecognized_res
Traceback (most recent call last):
  File "setup_RosettaCM.py", line 646, in <module>
    for name in thread_fullnames: assert (os.path.exists(name)), "File %s doesn't exist"%(name)
AssertionError: File /home/labusr/Desktop/chlamy_paper/denovo_prediction/alpha_tubulin/rosetta_cm/rosetta_cm/round_thread.pdb doesn't exist

 

I also tried the manual mode, with the grishin alignment that was successfully converted from setup_RosettaCM.py, I recieved the following error below:

 

[labusr@luxor rosetta_cm]$ ./manual_thread.sh 
core.init: Rosetta version rosetta.source.release-152:d6547f6858282e67c41356255dfdd63b0e7a75aa 2017-09-08 02:01:37.594540 from http://www.rosettacommons.org
core.init: command: /home/labusr/rosetta/main//source/bin/partial_thread.linuxgccrelease -in::file::fasta clustalw.fasta -in::file::alignment alignment.grishin -in::file::template_pdb alpha_tubulin_round_12.pdb
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-934584587 seed_offset=0 real_seed=-934584587
core.init.random: RandomGenerator:init: Normal mode, seed=-934584587 RG_type=mt19937
core.init: Resolved executable path: /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/partial_thread.default.linuxgccrelease
core.init: Looking for database based on location of executable: /home/labusr/rosetta/main/database/
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 557 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.37 seconds.
core.import_pose.import_pose: File 'alpha_tubulin_round_12.pdb' automatically determined to be of type PDB
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 36 in file alpha_tubulin_round_12.pdb. Best match rsd_type:  GLY
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 40 in file alpha_tubulin_round_12.pdb. Best match rsd_type:  GLU
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 41 in file alpha_tubulin_round_12.pdb. Best match rsd_type:  THR
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 42 in file alpha_tubulin_round_12.pdb. Best match rsd_type:  GLY
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CG  on residue GLU 40
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CD  on residue GLU 40
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OE1 on residue GLU 40
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OE2 on residue GLU 40
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OG1 on residue THR 41
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CG2 on residue THR 41
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 36 atom  CEN (trying to store temperature in PDBInfo)
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 40 atom  CEN (trying to store temperature in PDBInfo)
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 41 atom  CEN (trying to store temperature in PDBInfo)
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 42 atom  CEN (trying to store temperature in PDBInfo)
core.pack.pack_missing_sidechains: packing residue number 40 because of missing atom number 6 atom name  CG 
core.pack.pack_missing_sidechains: packing residue number 41 because of missing atom number 6 atom name  OG1
core.pack.task: Packer task: initialize from command line() 
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
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.
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.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
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/labusr/rosetta/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/labusr/rosetta/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.1 seconds to load from binary
core.pack.pack_rotamers: built 2 rotamers at 2 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 1492 bytes
partial_thread: [ ERROR ] can't find pose (id = round)

 

Post Situation: 
Wed, 2018-05-23 09:51
ahmadkhalifa

Any help would be much apprdciated. 

Wed, 2018-05-30 10:35
ahmadkhalifa

It's somewhat hard to say conclusively without seeing what's in the shell files you're using, but one thing I notice is that you're apparently using the Python which is installed with UCSF Chimera, as opposed to a standalone Python installation. This might cause issues. with the hash algorithms, depending on how the UCSF Chimera python was compiled.

On the second issue, the RosettaCM process is very particular about how things are named. You need to make sure that the names of the template PDBs, the names in the fastas, and the names in the alignments all match up appropriately. If they don't, that can lead to the issue you're seeing.

 

Thu, 2018-06-28 14:09
rmoretti