From f49375713883656e6baf94137942c8e8a9bd0d76 Mon Sep 17 00:00:00 2001
From: B13nch3n <b13nch3n_01@theb-si.de>
Date: Tue, 15 Nov 2022 16:46:08 +0100
Subject: [PATCH] Update README.md
---
README.md | 17 +++++++++++------
1 file changed, 11 insertions(+), 6 deletions(-)
diff --git a/README.md b/README.md
index df67ced..a355feb 100644
--- a/README.md
+++ b/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
-->
--
GitLab