diff --git a/README.md b/README.md index df67ced1c14b4049506d1ed00eda3fb896ebc8be..a355feb76f184189f44aeb6678b9183475da765c 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 -->