cg_annotate - Linux


cg_annotate is a versatile command in the cgkit suite, used for advanced annotation and analysis of crystallographic models. It allows for the addition of labels, annotations, and other metadata to crystallographic models, making them more informative and usable within the context of molecular modeling and simulation.


cg_annotate -i <input_model> [options] -o <output_model>


| Option | Required | Description | Default |
| -i | Yes | Path to the input crystallographic model file | – |
| -o | Yes | Path to the output annotated model file | – |
| -f | No | Annotation file format to use (pdb, mmcif, etc.) | pdb |
| -l | No | Path to the ligand library for annotation | – |
| -a | No | Label atoms with assigned b-factors | No |
| -A | No | Label atoms with calculated atomic displacement parameters (ADPs) | No |
| -c | No | Add comment lines to the output file | No |
| -d | No | Discard existing annotations from the input model | No |
| -h | No | Display help message and exit | – |


Simple Annotation

Annotate a PDB model (input.pdb) with residue names and atom names:

cg_annotate -i input.pdb -o output.pdb -l

Advanced Annotation

Label atoms with calculated ADPs and add comments to the output file:

cg_annotate -i input.pdb -o output.pdb -A -c

Common Issues

  • Incorrect input model format: Ensure that the input model file is in a supported format.
  • Annotation file format not supported: Specify the desired output annotation file format using the -f option.
  • Missing ligand library: Provide a path to the ligand library if annotations involving ligands are required.


  • MD simulations: Annotate models with atom labels for easier tracking during molecular dynamics simulations.
  • Structural analysis: Add metadata to models to facilitate automated analysis and comparison of structural features.
  • Model visualization: Generate models enhanced with annotations for more informative visualization in molecular graphics programs.

Related Commands