Written by Jean-Rémy Marchand

2 minute read

CAVIAR 1.1.0 is out!

CAVIAR now supports:

• cryoEM structures in mmCIF format
• iterative analysis of all models in NMR PDB files
• iterative analysis of all frames in a molecular dynamics file in DCD file format

A step-by-step tutorial for the new functionalities has been created in the advanced usage category –> on this page <–.

Here is a short summary:

mmCIF

I added a -cif option. If true, it will force finding mmCIF files rather than PDB, which might be an overkill. There is no metadata parser for the mmCIF file format yet, so I would advise to stick to PDB as much as it is possible for now.
If the option -cif is not set, CAVIAR will first look for a PDB file on RCSB PDB webservers, and then for CIF files, so it might still use a CIF file.
Moreover and importantly, a maximum grid size parameter has been set up at 10 million grid points, which represent about 12 gb of max memory usage. Therefore, some very large mmCIF structures might be rejected by default to avoid crashing: in that case, be sure to have a lot of RAM available, and increase the ‘size_limit’ parameter in a custom configuration file.

NMR structures

All NMR models in a PDB file are investigated iteratively, and a report is printed out for each model. Each model outputs its corresponding PDB file containing each its cavities/subcavities. Nothing needs to be done, CAVIAR recognizes automatically the NMR tag in the metadata to set up the routines.

DCD molecular dynamics trajectories

Similarly to NMR structures, all frames of a DCD trajectory file are processed iteratively. Each frame gets its own report and its own PDB file containing its cavities/subcavities. That can take a lot of disk space, so be sure to preprocess the trajectory files beforehand! Two arguments are needed for DCD trajectory files: the pdb file needs to be given (via -code) as reference coordinates, and -dcd is used to input the DCD file containing the frames (with path, if in another directory). More information in the dedicated article.

GUI

None of these functionalities were added to the GUI, and it is not clear to me if they should be. The GUI focuses on the simplest use case, and that also means keeping it to PDB files for now.

A huge thanks to the ProDy team. This code relies on their software, they are doing an amazing job.