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

[Anonymous]

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)

 

[Anonymous]

Any help would be much apprdciated. 

[Anonymous]

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.

 

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