From dd2de66164e74e87fd7080330f339979b3f679fd Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 3 Oct 2022 15:10:31 +0200
Subject: [PATCH] Update README.md

---
 README.md | 25 +++++++++++++++++++++++--
 1 file changed, 23 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 0c2a9d5..69f5e4d 100644
--- a/README.md
+++ b/README.md
@@ -1,13 +1,34 @@
 # Translate ColabFold PDB files into ModelCIF
 
-This Git repo holds a (containerised) application to format [PDB](http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html) files together with some extra data into [ModelCIF](https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Index/) files. Its primary target are [ColabFold](https://colabfold.mmseqs.com) projects, so together with the input PDB file, the ColabFold configuration is needed and scores.
+This Git repository holds a (containerised) application to format [PDB](http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html) files together with some extra data into [ModelCIF](https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Index/) files. Its primary target are [ColabFold](https://colabfold.mmseqs.com) projects, so together with the input PDB file, the ColabFold configuration is needed and scores.
 
-The actual translation script uses [OpenStructure](https://openstructure.org) to deal with some of the biological/ chemical data. To spare you the installation process, we provide a Docker container ready to convert your data.
+The actual translation script uses [OpenStructure](https://openstructure.org) to deal with some of the biological/ chemical data. To spare you the installation process, we provide a [Docker container](https://www.docker.com) ready to convert your data.
 
 [[_TOC_]]
 
 ## Get the translation app
 
+There are two ways to get the Docker container: pull it from our [GitLab registry](https://git.scicore.unibas.ch/schwede/ma-wilkins-import/container_registry) or build it from the [Dockerfile](Dockerfile) in this Git repository.
+
+<!-- 
+- pull from GitLab registry
+- build from Dockerfile
+ -->
+
 ## Run the translation app
 
+<!-- 
+- Docker command
+- volumes
+- output (cif files and score files)
+ -->
+
 ## Troubleshooting
+
+<!-- 
+- file permissions
+- build with your user ID
+ -->
+
+<!--  LocalWords:  ColabFold OpenStructure TOC
+ -->
-- 
GitLab