Visualize models and trajectories
Assembline can output models in several formats.
By default, the following formats are produced:
RMF format in the
models_rmf
directoryThe 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
optionto rebuild only the first copy of each series (often the asymmetric unit of the complex) use
--first_copy_only
or--copies 0
optionto rebuild specific copies use
--copies
option, e.g.--copies 0,1,7
option
Visualize the top model(s) in Chimera and Xlink Analyzer
Visualizing top models in Chimera and Xlink Analyzer will help to answer:
Are crosslinks satisfied?
Are there big clashes between subunits?
Are models fitting other information you have but not used in the optimization?
Visualize the optimization trajectory of the top model(s) in Chimera and Xlink Analyzer
The trajectories in the RMF format are stored in the
traj/
folder of the output directoryUCSF Chimera allows:
to open the RMF format and play the trajectories
display plots of the total score and individual restraints over the course of the trajectory
Analyze:
are all rigid bodies expected to move during the trajectory?
are the total scores and all restraints decreasing?
For better visualization of crosslinks and to color the subunits in the RMF by subunit color, you can use Xlink Analyzer.
Note
For Xlink Analyzer to work, you need to replace a file
share/rmf/__init__.py
in your Chimera installation with this file: https://github.com/crosslinks/XlinkAnalyzer/blob/master/edited__init__.py_for_chimera_rmfThe
share
directory is located within the Chimera installation folder (https://www.cgl.ucsf.edu/chimera/experimental/install.html):
source Windows C:\Program Files\Chimera\share Linux /usr/local/chimera/share Macintosh /Applications/Chimera.app/Contents/Resources/share