Visualize models and trajectories

Assembline can output models in several formats.

By default, the following formats are produced:

  • RMF format in the models_rmf directory

    The RMF files can be visualized in UCSF Chimera and UCSF ChimeraX

  • Simple TXT format that stores transformations of rigid bodies in the models_txt directory

In addition, optionally, trajectories of the optimization runs can be saved in the RMF format, in traj directory (using --traj option of assembline.py)

These two formats can be used to generate PDB or CIF files of the resulting integrative models, using rebuild_atomic.py atomic script.

Create CIF format file for top models

In the output directory, run:

rebuild_atomic.py --project_dir <full path to the original project directory> --top 1 all_scores_sorted_uniq.csv

Note

The --project_dir option is only necessary if you use relative paths in the JSON configuration file

Warning

This will only build the parts corresponding to rigid bodies, if had flexible beads in the system, see below how to rebuild them at the atomic resolution

Create CIF format file for a specific model

rebuild_atomic.py --project_dir <full path to the original project directory> --top 1 models_txt/0002321model.txt

Rebuilding flexible beads

If you had single residue flexible beads in your modeling (i.e. at representation resolution of 1), they can be rebuilt by running this script with --rmf and --rmf_auto option:

For the top models:

rebuild_atomic.py --project_dir <full path to the original project directory> --top 1 --rmf_auto all_scores_sorted_uniq.csv

For a specific model:

rebuild_atomic.py --project_dir <full path to the original project directory> --top 1 --rmf models_rmf/0002321model.rmf models_txt/0002321model.txt

The -rmf options tell the script to extract flexible beads from the RMF files and re-model them at atomic resolution using Modeller.

Create PDB for top models

rebuild_atomic.py --project_dir <full path to the original project directory> --top 1 --format pdb all_scores_sorted_uniq.csv

Warning

The PDB format is not recommended (especially for multi-subunit complexes) - it does not support multi-character chain IDs and has a limit on the number of atoms in the file.

Create separate PDB files for rigid bodies

rebuild_atomic.py --project_dir <full path to the original project directory> --top 1 --format multi_pdb all_scores_sorted_uniq.csv

This can be useful if you want to use the models for subsequent optimizations with Assembline or other software.

The scripts used for 3. Refinement are using the multi_pdb format behind the scenes.

Other options

See rebuild_atomic.py usage instructions for other useful options:

rebuild_atomic.py -h

For example:

  • to rebuild a specific subunit use --subunit option

  • to rebuild only the first copy of each series (often the asymmetric unit of the complex) use --first_copy_only or --copies 0 option

  • to rebuild specific copies use --copies option, e.g. --copies 0,1,7 option