Pre-packing a model for SWA loop building

[Anonymous]

Dear all,

I am trying to use one of the example scripts mentioned in the paper that first described the SWA method for protein loop building [Das, R. (2013). Atomic-accuracy prediction of protein loop structures through an RNA-inspired Ansatz. PLoS ONE 8, e74830], but it has been failing on me for reasons I do not understand.

The script is:

DATABASE="../../rosetta_2014.22.56873_bundle/main/database" 

BIN="../../rosetta_2014.22.56873_bundle/main/source/bin" 

SUFFIX="default.macosclangrelease" 

# 

${BIN}/swa_protein_main.${SUFFIX} -database $DATABASE -rebuild -out:file:silent_struct_type binary -fasta ../starting_files/1oyc.fasta -ccd_close -n_sample 18 -nstruct 400 -cluster:radius 0.100 -extrachi_cutoff 0 -ex1 -ex2 -score:weights score12.wts -pack_weights pack_no_hb_env_dep.wts -in:detect_disulf false -add_peptide_plane -native ../starting_files/1oyc_min.pdb -fixed_res 1-202 215-399 -superimpose_res 1-202 215-399 -rmsd_res 203-214 -jump_res 1 399 -disable_sampling_of_loop_takeoff -mute none -s1 ../starting_files/noloop_1oyc_min.pdb -input_res1 1-202 215-399 -use_packer_instead_of_rotamer_trials -ignore_unrecognized_res -out:file:silent ../output_files/REGION_215_202/START_FROM_START_PDB/region_215_202_sample.out  

When I run it using the above version of rosetta 3.5 (weekly release 2014.22.56873), I encounter the following error (below) right after some messages from the packer and a printout of the protein’s sequence as it is understood by rosetta:

  core.pack.task: Packer task: initialize from command line()

core.pack.pack_missing_sidechains: packing residue number 387 because of missing atom number 7 atom name CG core.scoring.ScoreFunctionFactory: SCOREFUNCTION: score12.wts

core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph

core.pack.pack_rotamers: built 177 rotamers at 1 positions. core.pack.pack_rotamers: IG: 1496 bytes S[SER:NtermProteinFull]FVKDFKPQALGDTNLFKPIKIGNNELLHRAVIPPLTRMRALHPGNIPNRDWAVEYYTQRAQRPGTMIITEGAFISPQAGGYDNAPGVWSEEQMVEWTKIFNAIHEKKSFVWVQLWVLGWAAFPDNLARDGLRYDSASDNVFMDAEQEAKAKKANNPQHSLTKDEIKQYIKEYVQAAKNSIAAGADGVEIHSANGYLLNQFLGSIENRARFTLEVVDALVEAIGHEKVGLRLSPYGVFNSMSGGAETGIVAQYAYVAGELEKRAKAGKRLAFVHLVEPRVTNPFLTEGEGEYEGGSNDFVYSIWKGPVIRAGNFALHPEVVREEVKDKRTLIGYGRFFISNPDLVDRLEKGLPLNKYDRDTFYQMSAHGYIDYPTYEEALKLGWDKK[LYS:CtermProteinFull] S[SER:NtermProteinFull]FVKDFKPQALGDTNLFKPIKIGNNELLHRAVIPPLTRMRALHPGNIPNRDWAVEYYTQRAQRPGTMIITEGAFISPQAGGYDNAPGVWSEEQMVEWTKIFNAIHEKKSFVWVQLWVLGWAAFPDNLARDGLRYDSASDNVFMDAEQEAKAKKANNPQHSLTKDEIKQYIKEYVQAAKNSIAAGADGVEIHSANGYLLNQFLGSIENRARFTLEVVDALVEAIGHEKVGLRLSPYGVFNSMSGGAETGIVAQYAYVAGELEKRAKAGKRLAFVHLVEPRVTNPFLTEGEGEYEGGSNDFVYSIWKGPVIRAGNFALHPEVVREEVKDKRTLIGYGRFFISNPDLVDRLEKGLPLNKYDRDTFYQMSAHGYIDYPTYEEALKLGWDKK[LYS:CtermProteinFull]

ERROR: option[ OptionKeys::stepwise::protein::protein_prepack ].user()

ERROR:: Exit from: src/apps/public/stepwise/enumerate/protein/swa_protein_main.cc line: 261

caught exception [ERROR]

EXCN_utility_exit has been thrown from: src/apps/public/stepwise/enumerate/protein/swa_protein_main.cc line: 261

ERROR: option[ OptionKeys::stepwise::protein::protein_prepack ].user()   

 The offending line 261 and following lines are pasted here for reference (the *** comment is mine): 

 // NOTE: These are new options that have been explored in StepWise MonteCarlo and are set to true...

// when we go back to stepwise enumeration, let's make sure user is forced to recognize this.

runtime_assert( option[ OptionKeys::stepwise::protein::protein_prepack ].user() ); *** line 261 ***

runtime_assert( option[ OptionKeys::stepwise::atr_rep_screen ].user() );

runtime_assert( option[ OptionKeys::stepwise::protein::allow_virtual_side_chains ].user() );  

Is there some option I am not aware of that I should have set to true in the script? Or is it something else entirely?

Many thanks in advance, best,

Francisco

[Anonymous]

That line is just checking if you have explicitly specified the -stepwise:protein:protein_prepack option on the commandline. (Is the option given “user” specified.) Either add “-stepwise:protein:protein_prepack true” or “-stepwise:protein:protein_prepack false” to your options file or commandline to fix the issue.
(SWA is under very active development at the moment, so the interface might be slightly different from that specified in the paper, requiring these additional options, so you” also have to be explicit about -stepwise:atr_rep_screen and -stepwise:protein:allow_virtual_side_chains too, probably along with other minor changes.)

BTW, Rosetta 3.5 is distinct from the weekly releases. Use the weekly release version specifier “2014.22.56873” *instead of* “3.5”, as opposed to in addition to.

[Anonymous]

Thanks for the reply and sorry about the confusion about the version number specifier, mine is indeed just the weekly release “2014.22.56873”.

Adding the options that you suggested in a stepwise fashion confirmed that all of them have to be present in the script for the pre-packer to work. In addition to those options, I also added -sampler_num_pose_kept 400 and -num_pose_minimize 400 instead of -out:nstruct 400 (the latter option is not recognised any more).

Thanks!

[Author]

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