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Structure Modification - Usage Guide

Overview

This skill covers modifying protein structures: transforming coordinates, removing/adding atoms and residues, modifying B-factors and occupancies, and building structures programmatically.

Prerequisites

pip install biopython numpy

Quick Start

Tell your AI agent what you want to do:

  • "Remove all water molecules from this structure"
  • "Translate the structure by 10 Angstroms in X"
  • "Set B-factors based on this conservation score data"

Example Prompts

Transformations

"Center this structure at the origin"

"Rotate the structure 90 degrees around the Z axis"

"Translate chain A by [10, 5, 0]"

Removing Entities

"Remove hydrogens from this structure"

"Delete chain B"

"Remove all hetero atoms (keep only protein)"

Modifying Properties

"Set all B-factors to 20"

"Color by conservation score in the B-factor column"

"Set occupancy to 0.5 for chain A"

Structure Building

"Renumber residues starting from 1"

"Rename chain A to X"

"Merge these two PDB files"

What the Agent Will Do

  1. Parse input structure(s)
  2. Navigate to target entities
  3. Apply requested modifications
  4. Save modified structure to new file

Key Operations

Operation Method
Remove atom residue.detach_child(atom_id)
Remove residue chain.detach_child(residue_id)
Remove chain model.detach_child(chain_id)
Transform Modify atom.coord directly
Modify B-factor Set atom.bfactor
Modify occupancy Set atom.occupancy
Rename chain Set chain.id
Renumber residue Set residue.id

Tips

  • Use detach_child() to remove entities, not del
  • Modify coord directly - atom.coord is a numpy array
  • B-factors for visualization - Use B-factor column to encode custom data
  • Chain IDs are single characters - typically A-Z
  • Residue ID is a tuple - (hetfield, resnum, icode)
  • Copy before modifying if you need to preserve original
  • StructureBuilder for building from scratch