RosettaCommons - Scoring

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Post Situation:

Abnormal output of ScoreCutoffFilter

DivingWhale — Fri, 31 May 2024 01:46:14 +0000

Hi everyone!

The output of `ScoreCuoffFilter` looks like this:
ResResE Res1 Res2 fa_atr fa_rep fa_sol fa_intra_r fa_intra_s lk_ball_wt fa_elec pro_close hbond_sr_b hbond_lr_b hbond_bb_s hbond_sc dslf_fa13 omega fa_dun p_aa_pp yhh_planar ref rama_prepr total
ResResE 83_6531 72_6532 -1.663 0.129 1.501 0.000 0.000 -0.424 0.258 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.198
....

The filed of Res1 or Res2 looks strange. In older version, this field will have the one-letter amino acid name, chain ID, and residue index. Why are name and chain ID replaced by numbers? Is there any update on this filter or it's replaced by other filter? I can't find documentation.

Rosetta version: rosetta.binary.linux.release-371

XML file:
<ROSETTASCRIPTS>
<SCOREFXNS>
</SCOREFXNS>
<RESIDUE_SELECTORS>
<Neighborhood name="nbrhood" resnums="35A-290A"/>
<Not name="others" selector="nbrhood" />
</RESIDUE_SELECTORS>
<TASKOPERATIONS>
<OperateOnResidueSubset name="turn_off_others" selector="others">
<PreventRepackingRLT/>
</OperateOnResidueSubset>
<RestrictToRepacking name="rtrp"/>
</TASKOPERATIONS>
<FILTERS>
<ScoreCutoffFilter name="scofilter" report_residue_pair_energies="1" cutoff="5000000.0" />
</FILTERS>
<SIMPLE_METRICS>
</SIMPLE_METRICS>

Could you please help me with this?

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Rosetta 3 - Applications

Post Situation:

Discrepancies between Foldit fa_rep score and Rosseta jd2 score fa_rep score

mrosam — Fri, 19 Apr 2024 14:57:58 +0000

Hi,

I'm analyzing the clashing between the residues of my protein and want to obtain a list of fa_rep scores for each of the residues of this protein. The thing is, when I score the model with rosetta_jd2 protocol the score of fa_rep that I obtain for the residues I'm interested in are around 0-3 REU and are not different from the rest of the structure. However, when I look at this protein in Foldit Standalone the fa_rep scores that I obtain for those residues are around 150-300 REU, while the rest of the molecule shows numbers of 0-5. I'm trying to understand where these discrepancies come from. IN the Foldit documentation they indicate that the scores are obtain from the ref2015 energy function of rosetta and that they may use some filters (which they don't describe).

The differences make sense to me, but I want to obtain similar results scoring directly through rosetta. How can I do that?

Thanks.

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Post Situation:

Scripts and/or strategies for saturation mutagenesis simulations?

drinker615 — Wed, 17 Apr 2024 01:43:46 +0000

Just wanted to confirm there is no semi-official script or protocol for DMS using Rosetta and ddg cartesian?

Seems like an easy enough thing to script using existing methods and protocols....but ideally, I would like a strategy that avoided generating 19 WT models per-site, per-iteration (since just one set would suffice for all DDGs).

That would same me a lot of comput time. For a 500aa protein with 10 iterations per DDG estimate, that would save me from building (18x500x10=90,000 superfulous models.

Does anyone have a suggestions (or a script) that can do this?

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Post Situation:

JD3 FastRelax over MPI - crashes on relax completion/before writing output

aduffy33 — Tue, 12 Mar 2024 19:51:57 +0000

Bit of a complicated issue here so apologies in advance if it's not entirely clear - happy to provide clarification.

I'm running a simple RosettaScripts file (relax_monomer_foldtree.rs_.xml_.txt) on one or more structures and am using JD3 to distribute the jobs (relax_jd3_S.xml_.txt). This works fine for small-to-moderately sized proteins and complexes (generally <1800 total amino acids in three chains of <600 each). However, for large proteins (i.e., full spike proteins; 3500+ total a.a.), this only works properly if all tasks are on the one node If tasks are split across 2+ nodes, the job will fail when the first task is completed but before the relaxed PDB is written with the following message:

[atl1-1-02-020-36-2.pace.gatech.edu:mpi_rank_12][async_thread] src/mpid/ch3/channels/mrail/src/gen2/ibv_channel_manager.c:1338: Got FATAL event local access violation work queue error on QP 0xea

[atl1-1-02-020-35-1.pace.gatech.edu:mpi_rank_2][handle_cqe] Send desc error in msg to 12, wc_opcode=0
[atl1-1-02-020-35-1.pace.gatech.edu:mpi_rank_2][handle_cqe] Msg from 12: wc.status=9 (remote invalid request error), wc.wr_id=0x15863a0, wc.opcode=0, vbuf->phead->type=24 = MPIDI_CH3_PKT_ADDRESS
[atl1-1-02-020-35-1.pace.gatech.edu:mpi_rank_2][mv2_print_wc_status_error] IBV_WC_REM_INV_REQ_ERR: This event is generated when the responder detects an invalid message on the channel. Possible causes include a) the receive buffer is smaller than the incoming send, b)  operation is not supported by this receive queue (qp_access_flags on the remote QP was not configured to support this operation), or c) the length specified in a RDMA request is greater than 2^31 bytes. It is generated on the sender side of the connection. Relevant to: RC or DC QPs.
[atl1-1-02-020-35-1.pace.gatech.edu:mpi_rank_2][handle_cqe] src/mpid/ch3/channels/mrail/src/gen2/ibv_channel_manager.c:497: [] Got completion with error 9, vendor code=0x8a, dest rank=12
: No such file or directory (2)
srun: error: atl1-1-02-020-36-2: task 12: Exited with exit code 255
srun: error: atl1-1-02-020-35-1: task 2: Exited with exit code 252
slurmstepd: error:  mpi/pmix_v3: _errhandler: atl1-1-02-020-36-2 [2]: pmixp_client_v2.c:212: Error handler invoked: status = -25, source = [slurm.pmix.4660380.0:12]

The relevant part appears to be the IBV_WC_REM_INV_REQ_ERR. Has anyone run into this before on their own MPI runs, and is it more likely to be a Rosetta problem or more of an MPI implementation problem on our end? Increasing RAM (initially at 8GB/cpu, all the way up to 32GB/cpu) does not appear to help.

Run command (slurm)

srun -JRelax $ROSETTA_PATH/bin/rosetta_scripts_jd3.cxx11threadmpiserialization.linuxgccrelease \
  -job_definition_file "$jd3" \
  -use_truncated_termini \
  -missing_density_to_jump \
  -jd3:n_archive_nodes 2 \
  -mpi_tracer_to_file logs/mpi \
  -linmem_ig 10 \
  -overwrite

Some specs:

RHEL 7.9, 8GB/cpu, 1 cpu/task (nstructs*pdbs + n_archive_nodes + 1 tasks), rosetta.source.release-340 compiled with mvapich2/2.3.6 & gcc/10.3.0 with mpi, serialization, and cxx11thread extras.

Attachment	Size
RosettaScripts file	532 bytes
JD3 jobfile	629 bytes

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Post Situation:

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Global Docking with output analysis RMS

kwu030 — Fri, 23 Feb 2024 17:17:57 +0000

Hello, Rosetta team

I performed global docking for two proteins and got the output.sc file, there are different "RMS"s reported, Irms, Irms_leg, cen_rms, rms, and st_rmsd, what values are more useful for analysis? I wonder if term "rms" is calcualted based on what? since I started with two far away proteins for global docking, I wonder if this rms is calcualted based on the intinial structure?

I did not provide native structure for global docking.

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Post Situation:

Error with SapScoreMetric (SimpleMetric sap_score not found in basic::datacache::DataMap)

Seongsung — Fri, 24 Nov 2023 13:09:32 +0000

Hello, I encountered an error while attempting to use the 'SapScoreMetric' in RosettaScript.

I encountered the following error, but when I exclude the 'SapScoreMetric' parts, it works well.

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

[ ERROR ]: An issue with your Rosetta run was detected

Please correct the following issue and retry:

SimpleMetric sap_score not found in basic::datacache::DataMap.

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

I installed the latest version of Rosetta (Rosetta 2023.45)

In my RosettaScript, I used 'SapScoreMetric' as shown below:

<SIMPLE_METRICS>

</SIMPLE_METRICS>

...

...

</PROTOCOLS>

and my command is as shown below:

/usr/bin/mpirun $ROSETTA3/bin/rosetta_scripts.cxx11threadmpiserialization.linuxgccrelease \
-parser:protocol inputs/my_script.xml \
-missing_density_to_jump \
-optimization::default_max_cycles 200 \
-jd2:failed_job_exception false \
-jd2:ntrials 1 \
-detect_disulf 1 \
-out:path:pdb results \
-nstruct 20 \
-l pdb_list

I would appreciate any advice or opinions.

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Rosetta 3 - Applications

Post Situation:

JD3 w/ Silent file output crashing - Option filename not found

aduffy33 — Mon, 30 Oct 2023 20:40:15 +0000

<Job nstruct="5">
     <Input>
          <PDB filename="pdb_basename.pdb" />
     </Input>
     <Output>
          <SilentFile path="pdb_basename" filename="pdb_basename_relaxed.silent"  />
     </Output>
     <SecondaryOutput>
          <ScoreFile path="pdb_basename" filename="score_pdb_basename.sc" />
     </SecondaryOutput>
     <Options>
          <parser__protocol value="path/to/RELAX_MONOMER_RS" />
     </Options>
</Job>

Apologies if this is the wrong category, couldn't quite determine which one this best fit into.

I'm using JD3 to run a protocol on multiple input PDBs (for now just FastRelax) and am trying to output all structures for a given input to a single silent file. However, whenever I try this with <Output> set to a silent file as above, Rosetta crashes & I get the following error (I've attached the full crash file as well):

[FILE]: src/utility/tag/Tag.hh
[LINE]: 182
[START_MESSAGE]
Option filename not found.

[END_MESSAGE]

When I replace the silent file with <PDB path="pdb_basename" filename_pattern="$_relaxed.pdb" /> the script runs as expected and outputs several relaxed PDBs in the folder pdb_basename; the issue just seems constrained to using SilentFiles, but I can't figure out the issue just based on the JD3 documentation (https://www.rosettacommons.org/docs/latest/RosettaScripts-JD3)

Thanks in advance for the help! Happy to provide more info as needed as well

Attachment	Size
Option filename not found log file.txt	6.65 KB

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Post Situation:

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Docking antibody to membrane protein

Yegor_Ko — Thu, 12 Oct 2023 14:37:53 +0000

Hello, what are the general guidelines for docking, when one of the protieins is a transmembrane and its partner is supposed to dock to the extracellular part (e.g. antibody or ligand)?

I suppose that the transmembrane one should be relaxed using MPFastRelax, whereas the extracellular using the standard REF15?
Which scoring function should be specified for docking?
Should one include any constraint to hide the intracellular and membrane part from docking or it's not necesary?
Are there any example protocols doing that?

Thank you in advance!

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Post Situation:

How do I compare the results of InterfaceAnalyzer using different trimers as input?

franz72 — Sun, 06 Aug 2023 17:10:00 +0000

Hi,

I hope you are having a nice weekend. I used the InterfaceAnalyzerMover using the interface option to calculate the change in free energy between chain A being bound or unbound to chains B and C. I then also calculated the binding affinity in the same way between chain B and chains A and C, and chain C and chains A and B. Can I take the mean of the three binding affinities I calculated to represent the binding affinity holding the trimer together? Can I compare the mean binding affinity of different trimers to one another using the same scoring function?

Thank you,

Franz

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Rosetta 3 - Applications

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