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structure-modification

separate

Modifies protein structures in place with Biopython Bio.PDB - transforms coordinates, strips waters/heteroatoms, overloads the B-factor column, renumbers, and builds entities. Use when applying a rotation matrix and needing to know whether it is row-convention (Entity.transform, Superimposer) or column-convention (REMARK 350 / _pdbx_struct_oper_list assembly operators) so geometry is not silently mirrored; when overloading B-factors with pLDDT/conservation for coloring and needing to preserve the destroyed originals; when stripping solvent by HETFLAG (r.id[0]) rather than residue name so catalytic metals and cofactors survive; and when building or copying entities through StructureBuilder/Select without breaking SMCRA parent-child links or the (hetflag, resseq, icode) id tuple. Keywords transform, rotation matrix, occupancy, assembly operators.

When to use

• transforming coordinates
• stripping waters and heteroatoms
• overloading B-factor column
• renumbering residues
• building entities
• applying rotation matrices
• handling assembly operators

When not to use

• using blanket HETFLAG to strip all heteroatoms
• stripping solvent by residue name instead of HETFLAG
• feeding column-convention matrices directly into Entity.transform without transposing

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