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 / pdbxstructoperlist 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.
Install with
Claude CodeCodexCursorGitHub CopilotGemini CLI
Supported by the Atlas install prompt. Skill-specific requirements vary.
Skill stats
Skills1CategoryScience & researchStars0
About this skill
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 / pdbxstructoperlist 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.
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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.
About this listing
Category
Science & research
Reported license
Not specified
Listing language (estimated)
English
Review status
Not individually reviewed
Agent compatibility
Atlas installation supports Claude Code, Codex, and Cursor. Skill-specific dependencies and features are checked during setup.
Claude Code
Codex
Cursor
GitHub Copilot
Gemini CLI