This page describes the flags that directly control the behavior of the RASREC module.
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.
| -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. |
There are several optional settings which have been benchmarked and tested thoroughly for optimal performance these options carry the comment "recommended":
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") |
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 |
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.
| -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) |