Update README.md

README.md

@@ -86,8 +86,8 @@ This container takes a directory of
 ColabFold models and turns them into 
 ModelCIF files.
 
-usage: translate2modelcif [-h] [--rank RANK] [--out_dir <OUTPUT DIR>]
-                          [--compress]
+usage: translate2modelcif [-h] [--selected_rank SELECTED_RANK]
+                          [--out_dir <OUTPUT DIR>] [--compress]
                           <MODEL DIR>
 
 Translate models from Tara/ Xabi from PDB + extra data into ModelCIF.
@@ -98,7 +98,11 @@ positional arguments:
 
 optional arguments:
   -h, --help            show this help message and exit
-  --rank RANK           Only process the model with this rank.
+  --selected_rank SELECTED_RANK
+                        If a certain model of a modelling project is selected
+                        by rank, the other models are still translated to
+                        ModelCIF but stored as accompanying files to the
+                        selected model.
   --out_dir <OUTPUT DIR>
                         Path to separate path to store results (<MODEL DIR>
                         used, if none given).
@@ -124,7 +128,7 @@ Running the converter app to write the ModelCIF file into a separated directory
 
 ```terminal
 $ mkdir /<PROJECTS PARENT DIR>/modelcif
-$ docker run --rm -v /<PROJECTS PARENT DIR>:/data registry.scicore.unibas.ch/schwede/ma-wilkins-import/converter:latest translate2modelcif --rank 1 --out_dir /data/modelcif /data/<UniProtKB AC>-<UniProtKB AC>
+$ docker run --rm -v /<PROJECTS PARENT DIR>:/data registry.scicore.unibas.ch/schwede/ma-wilkins-import/converter:latest translate2modelcif --selected_rank 1 --out_dir /data/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...
@@ -148,7 +152,7 @@ modelcif/
 
 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.
+If `--selected_rank` is omitted, all models in the project's directory are converted. Otherwise, still all models are converted but added to the Zip archive of the selected model.
 
 
 ## Troubleshooting
@@ -159,5 +163,6 @@ Depending on your local user/ permissions setup, it may happen that either the D
 
 <!--  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 mkdir
+      LocalWords:  builduserid ModelArchive
  -->