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Related Experiment Video

Updated: Jun 14, 2026

Manual Restraint and Common Compound Administration Routes in Mice and Rats

Manual Restraint and Common Compound Administration Routes in Mice and Rats

Published on: September 26, 2012

GEMMI and Servalcat restrain REFMAC5.

Keitaro Yamashita¹, Marcin Wojdyr², Fei Long¹

¹MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Trumpington, Cambridge CB2 0QH, United Kingdom.

Acta Crystallographica. Section D, Structural Biology

|May 9, 2023

Summary

This summary is machine-generated.

The CCP4 Monomer Library

Keywords:

GEMMI REFMAC5 Servalcat model refinement

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Area of Science:

Structural biology
Computational chemistry
Biochemistry

Background:

Macromolecular refinement requires chemical knowledge, typically geometrical restraints, to fit atomic models to experimental data.
The CCP4 suite stores this chemical knowledge in a Monomer Library using restraint dictionaries.
Restraints are used to infer atom-atom interactions and hydrogen atom positions during refinement.

Purpose of the Study:

To overhaul the process of using chemical knowledge in macromolecular refinement within the CCP4 suite.
To enhance the CCP4 Monomer Library with new features.
To improve the flexibility and ease of experimentation in structural modeling.

Main Methods:

Overhauling the process of analyzing models and inferring restraints from the Monomer Library.
Implementing new features within the Monomer Library.
Integrating the enhanced library into the REFMAC5 refinement program.

Main Results:

A more flexible and user-friendly system for applying chemical restraints in refinement.
Enhancements to the CCP4 Monomer Library.
A small but notable improvement in REFMAC5 refinement results.

Conclusions:

The overhaul of the CCP4 Monomer Library has significantly improved its usability and flexibility.
New library features contribute to better macromolecular refinement.
This advancement opens new avenues for structural modeling and experimentation.