README.md & fixes

README.md

@@ -62,7 +62,7 @@ $ DOCKER_BUILDKIT=1 docker build -t registry.scicore.unibas.ch/schwede/ma-wilkin
 
 `DOCKER_BUILDKIT=1` is only needed for some older versions of Docker.
 
-The Dockerfile knows two build time arguments (`--build-arg`), `MMCIF_USER_ID` and `ADD_DEV`. The latter is only used for developing the app. `MMCIF_USER_ID` sets the ID of the user running the translation script inside the Docker container. So files written by the Docker container belong to the user ID of the internal user. When you run into file permission issues with the produced ModelCIF files, build the Docker container using your own user ID:
+<a name="builduserid"></a>The Dockerfile knows two build time arguments (`--build-arg`), `MMCIF_USER_ID` and `ADD_DEV`. The latter is only used for developing the app. `MMCIF_USER_ID` sets the ID of the user running the translation script inside the Docker container. So files written by the Docker container belong to the user ID of the internal user. When you run into file permission issues with the produced ModelCIF files, build the Docker container using your own user ID:
 
 ```terminal
 $ DOCKER_BUILDKIT=1 docker build --build-arg MMCIF_USER_ID=<YOUR USER ID> -t registry.scicore.unibas.ch/schwede/ma-wilkins-import/converter:latest .
@@ -153,13 +153,11 @@ If `--rank` is omitted, all models in the project's directory are converted.
 
 ## Troubleshooting
 
-<!-- 
-- file permissions
-- build with your user ID
- -->
+### File permission problems
+
+Depending on your local user/ permissions setup, it may happen that either the Docker container cannot read or write the project directories. Otherwise, it can happen that files written by the app, are not readable for you on your local file system. This can be solved by building the Docker container with the same user ID as the local user executing the app. This is described [here](#builduserid)
 
 <!--  LocalWords:  ColabFold OpenStructure TOC schwede ccf cbfcc sha ceadc aaf
       LocalWords:  ae ddfc wilkins cd BUILDKIT arg DEV uid schwedelab modelcif
-<!--  LocalWords:  dir Xabi gzip unrelaxed pdb json config ACs CIF cif
- -->
+      LocalWords:  dir Xabi gzip unrelaxed pdb json config ACs CIF cif
  -->

docker-entrypoint.sh

@@ -9,13 +9,13 @@ set -euo pipefail
 ## usage.
 if [ $# -eq 0 ] || [ x$1 == x"-h" ] || [ x$1 == x"--help" ] ||
    [ x$1 == x"-help" ] || [ x$1 == x"help" ]; then
-    echo "      ModelCIF file formating tool."
+    echo "      ModelCIF file formatting tool."
     echo "------------------------------------------"
     echo "Provided by SWISS-MODEL / Schwede group"
     echo "(swissmodel.expasy.org / schwedelab.org)"
     echo ""
     echo "This container takes a directory of "
-    echo "AlphaFold2 models and turns them into "
+    echo "ColabFold models and turns them into "
     echo "ModelCIF files."
     echo ""
     /usr/local/bin/translate2modelcif --help

translate2modelcif.py

@@ -46,7 +46,9 @@ def _parse_args():
         + "'<UniProtKB AC>-<UniProtKB AC>'",
     )
     parser.add_argument(
-        "--rank", type=str, default=None, help="Only process top ranked model."
+        "--rank", type=str,
+        default=None,
+        help="Only process the model with this rank."
     )
     parser.add_argument(
         "--out_dir",
@@ -54,7 +56,7 @@ def _parse_args():
         metavar="<OUTPUT DIR>",
         default="",
         help="Path to separate path to store results "
-        "(model_dir used, if none given).",
+        "(<MODEL DIR> used, if none given).",
     )
     parser.add_argument(
         "--compress",