Update README.md

README.md

@@ -76,7 +76,7 @@ Replace `<YOUR USER ID>` with your own ID, e.g. after checking it with the `id`
 If you just run the Docker container, it prints a little usage description:
 
 ```terminal
-$ docker run registry.scicore.unibas.ch/schwede/ma-wilkins-import/converter:latest
+$ docker run --rm registry.scicore.unibas.ch/schwede/ma-wilkins-import/converter:latest
       ModelCIF file formatting tool.
 ------------------------------------------
 Provided by SWISS-MODEL / Schwede group
@@ -120,10 +120,10 @@ There can be more models for the same combination of the two UniProtKB ACs in a
 
 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 projects 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:
+Running the converter app to write the ModelCIF file into a separated directory  `modelcif` for model of rank 1 looks like this:
 
 ```terminal
-$ docker run -v /<PROJECTS PARENT DIR>:/data registry.scicore.unibas.ch/schwede/ma-wilkins-import/converter:latest translate2modelcif --rank 1 /data/<UniProtKB AC>-<UniProtKB AC>
+$ docker run --rm -v /<PROJECTS PARENT DIR>:/data registry.scicore.unibas.ch/schwede/ma-wilkins-import/converter:latest translate2modelcif --rank 1 --out_dir modelcif /data/<UniProtKB AC>-<UniProtKB AC>
 Let's go to the CIF site of life!
 Working on <UniProtKB AC>-<UniProtKB AC>...
   translating <UniProtKB AC>-<UniProtKB AC>_unrelaxed_rank_1_model_1.pdb...
@@ -136,18 +136,17 @@ Working on <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`):
+After this, you see two new files in the `modelcif` directory, the ModelCIF file (ending with `.cif`) and an archive with the pairwise alignment errors (ending with `.zip`):
 
 ```terminal
-<UniProtKB AC>-<UniProtKB AC>/
+modelcif/
 ├── <UniProtKB AC>-<UniProtKB AC>_unrelaxed_rank_1_model_1.cif
-├── <UniProtKB AC>-<UniProtKB AC>_unrelaxed_rank_1_model_1.pdb
-├── <UniProtKB AC>-<UniProtKB AC>_rank_1_model_1_scores.json
 ├── <UniProtKB AC>-<UniProtKB AC>_unrelaxed_rank_1_model_1.zip
-├── config.json
 └── ...
 ```
 
+With `--out_dir`, the converted files can be easily gathered for all projects and then handed over to the [ModelArchive](https://modelarchive.org) team to load them.
+
 If `--rank` is omitted, all models in the project's directory are converted.