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ACHESYM: an algorithm and server for standardized placement of macromolecular models in the unit cell
Marcin Kowiel1, Mariusz Jaskolski2, Zbigniew Dauter3
1Department of Organic Chemistry, Poznan University of Medical Sciences, Poznan, Poland.
Acta Crystallographica. Section D, Biological Crystallography
|December 6, 2014
Summary
A new program, ACHESYM, standardizes molecular model placement in crystallography unit cells. It implements the anti-Cheshire unit cell concept, resolving inconsistencies and improving structural data analysis.
Area of Science:
- Structural biology
- Crystallography
- Bioinformatics
Background:
- Standard conventions exist for unit cell and reciprocal space in crystallography.
- However, no standardized method exists for placing molecular models within the unit cell, causing inconsistencies.
Purpose of the Study:
- To introduce ACHESYM, a program and server for the practical implementation of the anti-Cheshire unit cell concept.
- To standardize molecular model placement in crystallographic unit cells.
- To optimize macromolecular assemblies when multiple polymer chains are present.
Main Methods:
- Implementation of the anti-Cheshire unit cell concept.
- Development of the ACHESYM program and web server.
- Processing of PDB and mmCIF files for atomic parameters, TLS matrices, and diffraction data.
Main Results:
- ACHESYM provides a standardized method for molecular model placement.
- The program identifies optimal (compact) macromolecular assemblies.
- ACHESYM can reindex reflections and modify phases as needed.
Conclusions:
- ACHESYM offers a practical solution to inconsistencies in molecular model placement in crystallography.
- This standardization facilitates clearer and more reliable structural data analysis.
- The tool aids in optimizing macromolecular assemblies for structural studies.
Keywords:
Cheshire symmetryanti-Cheshire unit cellbiological unitcrystallographic asymmetric unitoligomerquaternary structuresymmetry transformationMore Related Videos
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