RosettaCommons - Rosetta 3 - General

Post Situation:

Solved

FARFAR2 error: no edge found that contains seqpos!

mandar — Wed, 19 Jun 2024 01:39:06 +0000

Hi,

I am running MPI version of rna_denovo using command below using PDB, sequence, and secondary structure as inputs :

rna_denovo.mpi.linuxgccrelease -fasta rna_sequence.fasta -secstruct_general_file rna.secstruct -native 2CKY_1.pdb -align_pdb 2CKY_1.pdb -rmsd_screen 4.0 -cycles 20000 -minimize_rna true -nstruct 100 -out:file:silent FARFAR2_native_2CKY_1.out -use_legacy_job_distributor

However, this job is failed with no edge error as mentioned in ROSETTA_CRASH.log:

###################################

[FILE]: src/core/kinematics/FoldTree.cc
[LINE]: 2353
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: no edge found that contains seqpos!

#####################################

I could not trace origin of this error. Any suggestions to understand and solve this error would be of great help.

Thanks,

Mandar

Category:

Nucleic Acids

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Post Situation:

Error with fragment picking

gserci — Tue, 18 Jun 2024 00:37:39 +0000

Hello everyone,

I'm very new to using Rosetta and I'm having problems generating 3mers and 9mers. I've followed the tutorials and the documentation, but I continue to receive an error.

I've created a directory (input_files) with the following files: a FASTA sequence, an ss2 file (generated using PsiPred), and a PDB file (I've tried using both the one generated by AlphaFold3 and the one generated by DMPFold prediction but it doesn't seem to make a difference). The protein has 322 amino acids and I've verified that all three input files have 322 amino acids.

This is the command I use in the shell:

../../rosetta.binary.ubuntu.release-371/main/source/build/src/release/linux/5.4/64/x86/gcc/7/static/fragment_picker.static.linuxgccrelease @flags

And this is the contenute of "flags":

# Input databases
-in::file::vall                 ../../rosetta.binary.ubuntu.release-371/main/tools/fragment_tools/vall.apr24.2008.extended.gz

# Query-related input files
#-in::file::checkpoint          input_files/0296.checkpoint
-in::file::fasta                input_files/0296.fasta
-in::file::s                    input_files/0296.pdb
-frags::ss_pred                 input_files/0296.psipred.ss2 predA

# Weights file
-frags::scoring::config         input_files/simple.wghts

# What should we do?
-frags::bounded_protocol

# three-mers and nine-mers
-frags::frag_sizes              3 9
-frags::n_candidates            200
-frags::n_frags                 200

# Output
-out::file::frag_prefix         output_files/frags
-frags::describe_fragments      output_files/frags.fsc

This is the simple.wghts file:

# score name          priority  wght   max_allowed  extras
RamaScore               400    2.0     -       predA
SecondarySimilarity     350     1.0            predA
FragmentCrmsd             0     0.0     -

and this is the error in crash report:

[FILE]: src/protocols/frag_picker/scores/SecondarySimilarity.hh
[LINE]: 99
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to find secondary structure prediction for psipred

Lines 97-99 of SecondarySimilarity.hh are:

core::fragment::SecondaryStructureOP query_prediction( picker->get_query_ss(prediction_id) );
                if ( ! query_prediction ) {
                        utility_exit_with_message("Unable to find secondary structure prediction for " + prediction_id );

If I use, instead of simple.wghts:

SecondarySimilarity      350     0.5 - predA
ProfileScoreL1           50      1 -
FragmentCrmsd            30      0.0 -
RamaScore                100     2.0 - predA

this is the error:

[FILE]: src/protocols/frag_picker/scores/SecondarySimilarity.cc
[LINE]: 136
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Assertion `query_prediction->total_residue() == query_len_` failed.

Can you please help me making this fragment picker work?

Category:

Fragment Generation

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Post Situation:

Illegal attempt to score with non-identical atom set between pose and etable

ng98 — Fri, 07 Jun 2024 10:22:16 +0000

Hi! I am trying to use BlueprintBuilder to design based on the blueprint file. I wrote an xml file but it reports an error: core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 88 BB 1 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 45 BB 1 protocols.forge.remodel.RemodelMover: start stop cut cbreak protocols.forge.remodel.RemodelMover: 1 22 0 0 protocols.forge.remodel.RemodelMover: 36 49 44 17.8048 protocols.forge.remodel.RemodelMover: 60 96 87 32.5301 protocols.forge.remodel.RemodelMover: 109 141 114 20.4534 protocols.forge.remodel.RemodelMover: 153 166 153 4.11535 protocols.forge.remodel.RemodelMover: 175 228 0 0

ERROR: Illegal attempt to score with non-identical atom set between pose and etable pose atom_type_set: 'centroid' etable atom_type_set: 'fa_standard'

ERROR:: Exit from: src/core/scoring/etable/EtableEnergy.cc line: 281 protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:

File: src/core/scoring/etable/EtableEnergy.cc:281 [ ERROR ] UtilityExitException ERROR: Illegal attempt to score with non-identical atom set between pose and etable pose atom_type_set: 'centroid' etable atom_type_set: 'fa_standard'

protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job model-0.relaxed_0003_0001_0001

[ ERROR ]: Caught exception:

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

It seems like I am not using the right pdb but before I use the blueprintBuilder I used files in the demos/tutorials/full_atom_vs_centroid/flag_from_fa_to_cen to change my pdb into the centroid representation mode and it worked successfully. The attached file is my xml file. Could anyone please help me to solve this problem? Thank you!

Attachment	Size
bpBuilder_xml.txt	1.14 KB

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Post Situation:

Solved

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energy_based_clustering and silentfile option

weiw26 — Wed, 05 Jun 2024 23:28:59 +0000

I want to use energy_based_clustering to cluster structures from a silentfile. I run `source/bin/energy_based_clustering.linuxgccrelease @cluster_flag`.

Here cluster_flag is:

-in:file:silent ../global_output/decoys_P_renumbered_0001_traj.out
-in:file:fullatom
-cluster:energy_based_clustering:limit_structures_per_cluster 0
-cluster:energy_based_clustering:cluster_radius 2.0
-cluster:energy_based_clustering:cluster_by bb_cartesian
-cluster:energy_based_clustering:alternative_score_file input_score.txt
-cluster:energy_based_clustering:silent_output

-----------------------------------------------------------------------------

input_score.txt is the score file I prepared:

$ head input_score.txt

P_renumbered_0001_003_00000001 -5825.852
P_renumbered_0001_002_00000001 1107.339
P_renumbered_0001_001_00000001 8082.621
P_renumbered_0001_003_00000002 -5853.732
P_renumbered_0001_001_00000002 8072.546
P_renumbered_0001_002_00000002 1101.128
P_renumbered_0001_003_00000003 -5841.483

...

-----------------------------------------------------------------------------

When I run the clustering, I receive error message:

[FILE]: src/protocols/energy_based_clustering/EnergyBasedClusteringProtocol.cc
[LINE]: 1670
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to assign loaded score to pose 'P_renumbered_0001_001_00000001_../global_output/decoys_P_renumbered_0001_traj.out'. Please check your score file.

-----------------------------------------------------------------------------

I would like to get help on how to solve this error. Thanks

Category:

Scoring

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Post Situation:

Error about using BuildDeNovoBackboneMover

ng98 — Wed, 29 May 2024 08:47:05 +0000

Hi! I am sorry for asking about the segementation fault problems because this be caused by many things. It is the first time I wrote a Rosetta scripts and I really stuck on the script.

I tried to use BuildDeNovoBackboneMover to generate backbones based on the antibody structure I got, I wrote the xml file but it shows:

[FILE]: SIGSEGV
[LINE]: 11
[START_MESSAGE]

Segmentation Fault

[END_MESSAGE]
[END_CRASH_REPORT]

This is my XML file:

<ROSETTASCRIPTS>
        <SCOREFXNS>
                <ScoreFunction name="sfxn_16" weights="beta_nov16"/>
                <ScoreFunction name="sfxn" weights="beta_nov16"/>
        </SCOREFXNS>
        <RESIDUE_SELECTORS>
                <AntibodyRegion name="Abselect" region="cdr_region" cdr_definition="Chothia"/>
        </RESIDUE_SELECTORS>
        <TASKOPERATIONS>
                <AddCDRProfileSetsOperation name="AddCDRs" cdrs="all cdrs" include_native_restype="true" picking_rounds="3"/>
        </TASKOPERATIONS>
        <FILTERS>
                <ScoreType name="score_filter" score_type="sfxn_16" threshold="0" confidence="0"/>
                <ResidueCount name="res_count_all" max_residue_count="9999" confidence="0"/>
        </FILTERS>
        <MOVERS>
                <BuildDeNovoBackboneMover name="dn_backbone" dump_pdbs="false" >
                        <BlueprintArchitect name="bp_arch" blueprint="template1.bp"/>
                        <RemodelLoopMoverPoseFolder scorefxn="sfxn_16"/>
                </BuildDeNovoBackboneMover>
        </MOVERS>
        <APPLY_TO_POSE>
        </APPLY_TO_POSE>
        <PROTOCOLS>
                <Add mover="dn_backbone"/>
        </PROTOCOLS>
        <OUTPUT />
          
         
</ROSETTASCRIPTS>

My input is :rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease -parser:protocol blueprint_build.xml -corrections::beta_nov16 -s model-0.relaxed_0003.pdb -out:prefix test_

The model-0.relaxed_0003.pdb file is attached, I think it is because my input pdb or the blueprint file? But I do not know how to modify it based on my purpose. Could anyone please help me solve the problem? Thank you!

Attachment	Size
This is blueprint file.	1.16 KB
model-0.relaxed_0003.pdb	308.96 KB

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Post Situation:

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Is it impossible to use the ddg_monomer function on a non-monomeric structure?

Wexter300 — Sat, 25 May 2024 21:16:36 +0000

Hi,

I have been working on finding the most stable form of a tetrameric structure with 4 idenitical chains. I tried the ddg_monomer module. I could not get it to work using the original strucutre, but got it to work when I tried it with a single chain. Is there no way to get it to work with a tetramer? I have found an alternative using pmutscan to look for stabilizng mutations, but I would rather use ddg if possible. I was considering using ddg_monomer on a single chain and then just docking 4 of those mutated chains using rosetta_docking, but I don't know if that will take into account any interactions between reisudes in the tetramer structue that would not be accounted for when mutating only a single chain.

Much appreciated,

Wexte300

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Post Situation:

Question about blueprint file generation

ng98 — Fri, 24 May 2024 10:02:50 +0000

Hi, I am trying to use Rosetta to design an immunoglobulin structure based on the existing antibody structure. I read the paper :Chidyausiku,Tamuka M.,et al."De novo design of immunoglobulin-like domains".Nature Communications,vol.13,2022,https://doi.org/10.1038/s41467-022-33004-6. And I found in the paper that the backbone generation was made by Rosetta Monte Carlo fragment assembly using blueprints specifying secondary structures and ABEGO tor-
sion bins, together with hydrogen bond constraints specifying β-strand pairing. I used getBluePrintFromCoords.pl to get general blueprint file, but I was confused about following steps.

I got the general blueprint file like this:

1 Q .
2 V .
3 Q .
4 L .
5 V .
6 Q .
7 S .
8 G .
9 S .
10 E .
11 L .
12 K .
13 K .
14 P .
15 G .
16 A .
17 S .
18 V .
19 K .

.......
But I got problems about how to modify this general blueprint file, for example: how to determine which residue could be rebuilt or leave it alone; how to decide which residue shoulld be insert in which place? Are there any tutorials or paper that I could learn to get detailed explanations on how to build blueprint files? Or are there any movers or tools that I could use to help me solve those problems? I would appreciate if someone could help me on these questions. Thank you so much!

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Post Situation:

Error about rifdocking step 19 motifgraft mover

ng98 — Wed, 22 May 2024 09:25:18 +0000

Hi I've got provblem with Rifdocking protocol 19 when I test one of commands:

protocols.jd2.JobDistributor: [ WARNING ] mot_ferr_ems_00043_000000149_0001_58_64_E_HHHH_bc_01900_0001 reported failure and will NOT retry protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER MotifGraft - motif_grafting======================= protocols.motif_grafting.movers.MotifGraftMover: Executing Motif Graft Mover protocols.motif_grafting.movers.MotifGraftMover: Target scaffold size: 65 protocols.motif_grafting.movers.MotifGraftMover: Motif size: 7 protocols.motif_grafting.movers.MotifGraftMover: contextStructure size: 211 protocols.motif_grafting.movers.MotifGraftMover: Target scaffold numChains: 1 protocols.motif_grafting.movers.MotifGraftMover: Motif numChains: 1 protocols.motif_grafting.movers.MotifGraftMover: contextStructure numChains: 1 protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 7 protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] For this scaffold & fragment/size combination there are not fragments that match the size of your motifs. protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:

File: src/protocols/motif_grafting/movers/MotifGraftMover.cc:546 For this scaffold there are not suitable scaffold grafts within your constrains protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job mot_ferr_ems_00043_000000149_0001_58_64_E_HHHH_bc_01944_0001

[ ERROR ]: Caught exception:

File: src/protocols/motif_grafting/movers/MotifGraftMover.cc:546 For this scaffold there are not suitable scaffold grafts within your constrains

I followed the protocol and my command shown below: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease -parser:protocol /home/gaon/cao_protocol/cao_2021_protocol/paper_motif_graft.xml -beta_nov16 -in:file:silent /home/gaon/TYRP1/protocol/rifgen63_263/fd_output_splits/scaffold_splits/xah.silent -keep_input_scores False -silent_read_through_errors -out:file:silent out.silent -out:file:silent_struct_type binary -mute protocols.rosetta_scripts.ParsedProtocol.REPORT -parser:script_vars CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol @/home/gaon/TYRP1/protocol/rifgen63_263/fd_output_splits/grafting.flags -parser:script_vars motifpdb=/home/gaon/TYRP1/protocol/rifgen63_263/fd_output_splits/motifing/motifs/mot_ferr_ems_00043_000000149_0001_58_64_E.pdb.gz hotspots=1:2:3:4:5:6:7 -out:prefix mot_ferr_ems_00043_000000149_0001_58_64_E_

Could anyone please tell me why this error happened? Could it be fixed or just because something else? I will appreciate for the help. Thank you!

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Question about computer specifications requirement of RFdiffusion

ng98 — Mon, 06 May 2024 09:18:54 +0000

Hi! I would like to use RFdiffusion for binder design, but I wonder if there is any computer specifications requirement for running this deep learning model? Thank you for your help.

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