Translate models from Tara/ Xabi from PDB + extra data into ModelCIF.
positional arguments:
<MODEL DIR>Directory with model(s) to be translated. Must be of
form '<UniProtKB AC>-<UniProtKB AC>'
optional arguments:
-h, --help show this help message and exit
--rank RANK Only process the model with this rank.
--out_dir <OUTPUT DIR>
Path to separate path to store results (<MODEL DIR>
used, if none given).
--compress Compress ModelCIF file with gzip (note that QA file is
zipped either way).
```
To actually run the conversion, we assume the ColabFold projects are separated into individual directories. Project directories have to look like this:
There can be more models for the same combination of the two UniProtKB ACs in a directory, the above example just shows the minimum required files.
Since the Docker container does not see the file system of the computer it is running on, the top level directory of the projects needs to be mounted when running. This happens with the `-v` option and gets absolute paths to the project directory and the mount point inside the Docker container, e.g. `-v /path/to/projects:/data` makes the directory `/path/to/projects` on your computer, available as `/data` to the Docker container.
Running the converter app to write the ModelCIF file back into the project directory for model of rank 1 looks like this:
... done with /data/<UniProtKB AC>-<UniProtKB AC>/<UniProtKB AC>-<UniProtKB AC>_unrelaxed_rank_1_model_1.pdb (55.61s).
... done with /data/<UniProtKB AC>-<UniProtKB AC>.
$
```
After this, you see two new files in the project's directory, the ModelCIF file (ending with `.cif`) and an archive with the pairwise alignment errors (ending with `.zip`):
