An introductory tutorial on packing can be found here, and on protein design can be found here.
Rotamer Packing options can be used in fixed backbone design mode and other protocols. For most Rosetta protocols, the flags
-ex1 -ex2 -use_input_sc are sufficient and should be added to the command line. Please read the documentation for each protocol as this may not be useful for some.
-packing:ex1 Use extra chi1 sub-rotamers for all residues that pass the extrachi_cutoff. [Boolean]
-packing:ex1:level Use extra chi1 sub-rotamers for all residues that pass the extrachi_cutoff. [Integer]
legal=[ '0', '1', '2', '3', '4', '5', '6', '7' ]
The integers that follow the ex flags specify the pattern for chi dihedral angle sampling.
There are currently 8 options; they all include the original chi dihedral angle.
NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all
EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples
EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples
EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples
EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples
EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples
EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples
EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples.
-packing:ex1:operate Apply special operations (see RotamerOperation class) on ex1 rotamers. [Boolean]
-packing:ex2 Use extra chi2 sub-rotamers for all residues that pass the extrachi_cutoff.
-packing:ex2:level Use extra chi2 sub-rotamers for all residues that pass the extrachi_cutoff.
The integers that follow the ex flags specify the pattern for chi dihedral angle sampling.
There are currently 8 options; they all include the original chi dihedral angle.
NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all
EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples
EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples
EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples
EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples
EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples
EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples
EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
-packing:ex1:operate Apply special operations (see RotamerOperation class) on ex2 rotamers. [Boolean]
-packing:ex3 Use extra chi3 sub-rotamers for all residues that pass the extrachi_cutoff.
-packing:ex3:level Use extra chi3 sub-rotamers for all residues that pass the extrachi_cutoff.
The integers that follow the ex flags specify the pattern for chi dihedral angle sampling.
There are currently 8 options; they all include the original chi dihedral angle.
NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all
EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples
EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples
EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples
EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples
EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples
EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples
EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
-packing:ex3:operate Apply special operations (see RotamerOperation class) on ex3 rotamers. [Boolean]
-packing:ex4 Use extra chi4 sub-rotamers for all residues that pass the extrachi_cutoff.
-packing:ex4:level Use extra chi4 sub-rotamers for all residues that pass the extrachi_cutoff.
The integers that follow the ex flags specify the pattern for chi dihedral angle sampling.
There are currently 8 options; they all include the original chi dihedral angle.
NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all
EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples
EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples
EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples
EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples
EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples
EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples
EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
-packing:ex4:operate Apply special operations (see RotamerOperation class) on ex4 rotamers. [Boolean]
-packing:extrachi_cutoff Number of neighbors a residue must have before extra rotamers are used. default: 18 [Integerx]-packing:ex1aro Use extra chi1 sub-rotamers for aromatic residues that pass the extrachi_cutoff. [Boolean]
-packing:ex1aro:level Use extra chi1 sub-rotamers for all residues that pass the extrachi_cutoff.
The integers that follow the ex flags specify the pattern for chi dihedral angle sampling.
There are currently 8 options; they all include the original chi dihedral angle.
NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all
EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples
EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples
EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples
EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples
EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples
EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples
EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
-packing:ex2aro Use extra chi2 sub-rotamers for aromatic residues that pass the extrachi_cutoff.
-packing:ex2aro:level Use extra chi2 sub-rotamers for all residues that pass the extrachi_cutoff.
The integers that follow the ex flags specify the pattern for chi dihedral angle sampling.
There are currently 8 options; they all include the original chi dihedral angle.
NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all
EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples
EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples
EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples
EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples
EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples
EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples
EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
-packing:ex1aro_exposed Use extra chi1 sub-rotamers for all aromatic residues. [Boolean]
-packing:ex1aro_exposed:level Use extra chi1 sub-rotamers for all aromatic residues that pass the extrachi_cutoff.
The integers that follow the ex flags specify the pattern for chi dihedral angle sampling.
There are currently 8 options; they all include the original chi dihedral angle.
NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all
EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples
EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples
EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples
EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples
EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples
EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples
EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
-packing:ex2aro_exposed Use extra chi2 sub-rotamers for all aromatic residues. [Boolean]
-packing:ex2xaro_exposed:level Use extra chi2 sub-rotamers for all aromatic residues that pass the extrachi_cutoff.
The integers that follow the ex flags specify the pattern for chi dihedral angle sampling.
There are currently 8 options; they all include the original chi dihedral angle.
NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all
EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples
EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples
EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples
EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples
EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples
EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples
EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples-packing:resfile Resfile filename(s). Most protocols use only the first and will ignore the rest;
it does not track against -s or -l automatically.
Default='resfile' [FileVector]-packing:no_optH Do not optimize hydrogen placement at the time of a PDB load. default="true" [Boolean]
-packing:pack_missing_sidechains Run packer to fix residues with missing sidechain density at PDB load. default="true"
[Boolean]
-packing:fix_his_tautomer Seqpos numbers of his residus whose tautomer should be fixed during repacking.
[IntegerVecter]
-packing:use_input_sc Use rotamers from input structure in packing. By default, input sidechain coords are NOT
included in rotamer set but are discarded before the initial pack; with this flag, the input
rotamers will NOT be discarded. Note that once the starting rotamers are replaced by any mechanism,
they are no longer included in the rotamer set. (rotamers included by coordinates)
-packing:linmem_ig Force the packer to use the linear memory interaction graph; each RPE may be computed more than once,
but recently-computed RPEs are reused. The integer parameter specifies the number of recent rotamers
to store RPEs for. 10 is the recommended size. Memory use scales linearly with the number of rotamers
at about 200 bytes per rotamer per recent rotamers to store RPEs for(~4 KB per rotamer by default).
default='10' [Integer]
-packing:no_his_his_pairE Set pair term for His-His to zero. [Boolean]
-packing:solvate Add explicit water, but don't try to place water such that it bridges Hbonds, just put it on every
available Hbond donor/acceptor where there's no clash (implies explicit_h2o). [Boolean]
-packing:multi_cool_annealer Alternate annealer for packing. Runs multiple quence cycles in a first cooling stage, and tracks the N
best network states it observes. It then runs low-temperature rotamer substitutions with repeated quenching
starting from each of these N best network states. 10 is recommended.