Flags (RASREC)

This page describes the flags that directly control the behavior of the RASREC module.

Input Options

RASREC uses the abrelax protocol via the BROKER interface, and can iteratively assign NOESY crosspeaks using the AutoNOE module. All input files are handled by the respective modules directly and their flags are described in the respective Module Sections.

Changed Interpretation of output options

-out:nstruct 100 controls how many structures are produced per batch, ideally this is set to the number of worker processes (that is total number of processors - 3). The total number of structures produced depends on the number of batches started by RASREC and cannot be directly controlled by the user
-out:file:silent dummy.out For technical reasons it is important that the option -out:file:silent is present in the cmd-line. However, the chosen name, here dummy.out, will be ignored. RASREC writes structures into subdirectories (batch_xxx and xxx_pool) of the working directory and always uses the file-name 'decoys.out' for this.

Algorithmic options

There are several optional settings which have been benchmarked and tested thoroughly for optimal performance these options carry the comment "recommended":

Stage Control

This group of options controls, how the RASREC algorithm switches through the different resampling stages.

-iterative:fullatom run fullatom stages V and VI (recommended)
-iterative:min_diversity Accept only structures into the archive that are at least X Angstrom different from previously added structures (recommended "0 0 0 2 3 2 2 1.5").
-iterative:max_nstruct always switch to next stage, if a maximum number of structures is reached, -1 skip stage, 0 infinite number of structures(recommended "0 0 0 0 0 0")
-iterative:accept_ratio switch to next stage, if acceptance ration into the archive drops below the respective threshold value. Raising this would result in a decrease of the total number of structures produced, because RASREC would switch earlier to next stage. (recommended "0.1 0.1 0.1 0.1 0.1 0.1")

Resampling Control

This group of options controls, how the RASREC resampling batches are generated.

-iterative:enumerate:broker allows to define custom setup for jumping during enumerated pairing batches (stage I+II). Usually, this is not specified and RASREC automatically generates suitable pairings based on secondary structure.
-iterative:enumerate:skip_half run half of the batches without enumerated pairings(recommended).
-iterative:initial_beta_topology use the given topology file to seed the topology resampling (stage III). Usually this is used in conjunction with -iterative:max_nstruct -1 -1 0 0 0 0, to start the RASREC simulation directly in stage III.
-iterative:force_topology_resampling Forces to run through stages I-III. This overrides the default behavior, which skips these stages, if there are less than 40 strand-residues which also make up less than 15% of the total protein
-iterative:recompute_beta_Naccept recompute beta-topology after minimum of Naccept structures -- if no initial_beta_topology always recompute
-iterative:mix_frags mix frags with original fragset
-iterative:safety_hatch_scorecut in CEN2FULLATOM state use structures for input that are below scorecut in individual batches

Evaluation and Selection

This group of flags controls how structures are evaluated to decide whether or not they can be accepted into the archive of low-energy structures.

Processing options

For running multiple jobs on a cluster the following options are useful:

-iterative:cen_score energy function for centroid pool (default: score3)
-iterative:cen_score_patch patch of centroid_pool energy function (e.g., to add restraint scores to selection)
-iterative:fa_score energy function for centroid pool (default: score12_full)
-iterative:fa_score_patch patch of fullatom_pool energy function (e.g., to add restraint scores to selection)
-iterative:centroid_quickrelax run a quick relax protocol even on centroid structures. This step is already done automatically, if chemical shift score is used for final selection (-iterative:cenpool_chemicalshif_weight) or if run in autoNOE mode, since both modes require all-atom information to be present.
-iterative:super_quick_relax_protocol provide a sequence file for super quick relax protocol to overwrite standard protocol. This can, e.g., be used to reduce the super-quick relax protocol to mere repacking of sidechains.
-iterative:centroid_before_quickrelax_weight for selection into the centroid pool, weight of the centroid score (score3) of the decoy before it was passed to the super-quick relax protocol.
-iterative:fullatom_after_quickrelax_weight for seleciton into the centroid pool one can also use the full-atom score of the 'super-quick relaxed' structures. With the standard protocol for super-quick relax these scores are usually not very well refined and our recommendation is 0.0 (default) for this weight.
-iterative:cenpool_chemicalshift_weight weight to apply to chemical shifts in centroid pool rescoring. Works only if also the flag '-evaluation:chemical_shifts cs.tab chem_shifts' is present.
-iterative:fapool_chemicalshift_weight weight to apply to chemical shifts in fullatom pool rescoring
-iterative:chemicalshift_column column name of the ChemicalShiftEvaluator used for chemical shift rescoring -- allows to have inactive shifts in score (default: 'chem_shifts')
-iterative:flags_fullatom a flag-file that specifies how to run loop-closing and fullatom-refinement. Required for full-atom stages V+VI.
-iterative:normalize:sampling use normalized restraint weights for sampling during centroid stage sampling
-iterative:rmsf_nstruct RASREC determines converged regions from the N lowest structures in the archive. These cores are used for RMSD calculation and are for information purposes only. This flag controls N.
-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)