An application that uses the abinitio protocol and is, for example, started in the directory rosetta_demos/abinitio/ would read-out the following flags:
| -in:file:native ./input_files/1elw.pdb | Native structure (optional) |
| -in:file:fasta ./input_files/1elwA.fasta | Protein sequence in fasta format (required) |
| -in:file:frag3 ./input_files/aa1elwA03_05.200_v1_3 | Fragment library: 3-residue fragments (required) |
| -in:file:frag9 ./input_files/aa1elwA09_05.200_v1_3 | Fragment library: 9-residue fragments (required) |
| -database ../../rosetta_database | Path to rosetta database (required if not ROSETTA3_DB environment variable is set) |
| -nstruct 1 | Number of output structures (default=1). |
| -out:file:silent 1elwA_silent.out | Use silent file output, use filename after this flag (default=default.out). |
| (or -out:pdb) | Use PDB file output (default=false). |
| -out:path /my/path | Path where PDB output files will be written to (default='.'). |
These flags are implemented in FragmentSampler .cc
There are several optional settings which have been benchmarked and tested thoroughly for optimal performance these options carry the comment "recommended":
| -abinitio::increase_cycles 10 | Increase the number of cycles at each stage in ab initio by this factor (recommended). |
| -abinitio:rg_reweight 0.5 | Reweight contribution of radius of gyration to total score by this scale factor (recommended). |
| -abinitio:rsd_wt_helix 0.5 | Reweight env,pair,cb for helix residues by this factor (recommended). |
| -abinitio:rsd_wt_loop 0.5 | Reweight env,pair,cb for loop residues by this factor (recommended). |
| -abinitio:stage1_patch | Supply patch file for the score0 ScoreFunction used in Stage1 |
| -abinitio:stage2_patch | Supply patch file for the score1 ScoreFunction used in Stage2 |
| -abinitio:stage3a_patch | Supply patch file for the score2 ScoreFunction used in Stage3 |
| -abinitio:stage3b_patch | Supply patch file for the score5 ScoreFunction used in Stage3 |
| -abinitio:stage4_patch | Supply patch file for the score3 ScoreFunction used in Stage4 |
| -abinitio:skip_stages 1 2 3 4 | list all stages (1-4) that should be skipped (default=None) |
| -abinitio:recover_low_in_stages 1 2 3 4 | after the sampling cycles of a given block are finished the lowest scoring pose recorded during the sampling is recovered, use this flag to switch this off for individual stages |
These flags are implemented in ConstraintFragmentSampler .cc
| -constraints:cst_weight 1.0 | Patches the weight for the ScoreType atom_pair_constraint in all scores (score0, score1, score2, score5 and score3) used for abinitio. This change is applied after patching via -stageX_patch. |
| -fold_cst:seq_sep_stages f1 f2 f3 | Restraints and chainbreak-penalties are considered based on their sequence separation. The maximum sequence separation an active restraint can have is slowly ramped up. The target values for the ramping can be controlled for the end-points of stage 2, 3 and 4, and are given as fraction of total length of protein (default=0.15, 1.0, 1.2). |
| -fold_cst:skip_on_noviolation_in_stage1 | In Stage1 the maximum restraint sequence separation is incremented in steps of 2 residues. After each increment a block of sampling cycles is performed. This option allows to terminate (or skip) sampling no restraint is violated at a given time. |
| -constraint:threshold | control the threshold above which a constraint is violated (default=1). |
| -fold_cst:no_recover_low_at_constraint_switch | When new constraints are turned (seq_sep_stages) the MonteCarlo object has to be reset and the previously found lowest energy pose will be lost. To avoid loosing this information, we usually carry out a recover_low before switching on new constraints. Use this flag to avoid this extra recover_low. |
| -jumps:ramp_chainbreaks | smoothly ramp up the weights for ScoreTypes linear_chainbreak and overlap_chainbreak (recommended, default=true). |
| -jumps:increase_chainbreak | factor for the ramping of chainbreaks (default=1.0). |
| -jumps:overlap_chainbreak | use the overlap chainbreak in stage4 (recommended, default=false). |
| -jumps:chainbreak_weight_stage1 | Set the weight for ScoreType linear_chainbreak for Stage1. Irrelevant if ramping of chainbreaks is active. |
| -jumps:chainbreak_weight_stage2 | Set the weight for ScoreType linear_chainbreak for Stage2. Irrelevant if ramping of chainbreaks is active. |
| -jumps:chainbreak_weight_stage3 | Set the weight for ScoreType linear_chainbreak for Stage3. Irrelevant if ramping of chainbreaks is active. |
| -jumps:chainbreak_weight_stage4 | Set the weight for ScoreType linear_chainbreak for Stage4. Irrelevant if ramping of chainbreaks is active. |
For running multiple jobs on a cluster the following options are useful:
| -constant_seed | Use a constant seed (1111111 unless specified with -jran) |
| -jran 1234567 | Specify seed. Should be unique among jobs (requires -constant_seed) |
| -seed_offset 10 | This value will be added to the random number seed. Useful when using time as seed and submitting many jobs to a cluster. If jobs are started in the same second they will still have different initial seeds when using a unique offset. If using Condor (http://www.cs.wisc.edu/condor), the Condor process id, $(Process), can be used for this. For example "-seed_offset $(Process)" can be used in the condor submit file. |
| -run:dry_run | no sampling cycles, just initialize all objects (for testing, default=False) |
| -run:test_cycles | only a single sampling cycle per stage (for testing, default=False) |