Packing

Use this compact recipe for fixed-sequence repacking. The linked tutorial develops local repacking and explicitly scoped mutation or design experiments.

• Prerequisites: A prepared PoseStack and a score function built from the same parameter database.

• Deep tutorial: 04 — Packing and Mutation Scan.

• Related workflows: Optimization and Nucleic acids.

• API reference: Packing and Relax.

• Rosetta mapping: Packing, design, and mutation scans.

Fixed-sequence repacking searches side-chain or nucleic-acid chi conformers without changing block identity. The usual workflow creates a PackerTask, restricts it to repacking, attaches rotamer samplers, and calls pack_rotamers(). Mutation or sequence design requires explicit identity masks; TMol does not provide Rosetta resfiles or a built-in mutation-scan protocol.

from tmol.pack import pack_rotamers
from tmol.pack import PackerPalette, PackerTask
from tmol.pack.rotamer.dunbrack import (
    create_dunbrack_sampler_from_database,
)
from tmol.pack.rotamer import FixedAAChiSampler
from tmol.pack.rotamer import IncludeCurrentSampler

task = PackerTask(pose_stack, PackerPalette())
task.restrict_to_repacking()
task.add_conformer_sampler(
    create_dunbrack_sampler_from_database(context.parameter_database, device)
)
task.add_conformer_sampler(FixedAAChiSampler())
task.add_conformer_sampler(IncludeCurrentSampler())

packed_pose_stack = pack_rotamers(pose_stack, sfxn, task)

To keep a subset of residues fixed, build a boolean block mask and disable packing for those blocks:

task.disable_packing_by_block_mask(fixed_block_mask)

The protein-ligand refinement example uses this pattern to repack protein side chains while holding the ligand block fixed.

restrict_to_repacking() intersects the task with each block’s original identity. Mutation or design therefore needs an explicitly constructed identity task instead of this fixed-sequence recipe. FastRelax composes packing with minimization, while 08 — Working with DNA and RNA uses an NA-specific chi sampler and explicit masks.