diff --git a/projects/human-heterodimers-w-crosslinks/README.md b/projects/human-heterodimers-w-crosslinks/README.md index 637dbe6e8b608b8da702067d12b41e13c115ed33..73a40bdc99f0a75ae26e03116423f825c85908ce 100644 --- a/projects/human-heterodimers-w-crosslinks/README.md +++ b/projects/human-heterodimers-w-crosslinks/README.md @@ -1,6 +1,6 @@ # Modelling protein-interactions of human proteins with experimental crosslinking information -**I.O.U. the link to the ModelArchive entry** +[Link to project in ModelArchive](https://www.modelarchive.org/doi/10.5452/ma-low-csi) (incl. background on project itself) **I.O.U. the link to the publication** @@ -35,9 +35,9 @@ These models qualify as "de novo modelling". ### Special features - For changed sequences of UniProtKB entries by an UniProtKB update -- Search history of an UniProtKB entry for a matching sequence -- Version in ModelCIF will be with the latest matching sequence -- Please note: this mechanism is only and solely meant for different versions of UniProtKB sequences, it is not usable with user modified sequences, user modified sequences will make the conversion script crash + - Search history of an UniProtKB entry for a matching sequence + - Version in ModelCIF will be with the latest matching sequence + - Please note: this mechanism is only and solely meant for different versions of UniProtKB sequences, it is not usable with user modified sequences, user modified sequences will make the conversion script crash - Converter script is able to deal with selenocysteine (missing residue in models/ not modelled by ColabFold) - Uses UniProtKB AC if gene name is missing for a UniProtKB entry @@ -45,8 +45,8 @@ These models qualify as "de novo modelling". ### Usage - The [conversion script](./translate2modelcif.py) runs on a single target (modelling project) directory, if you have multiple targets, like in a whole proteome, you need to loop over the directory and call the script for each separately -- Output can be written either to the model directory or a separated directory (`--out`) -- In this project, for each dimer only one model is stored at [ModelArchive](https://modelarchive.org/) (MA) but the other models for the same dimer are stored in a Zip archive that goes into MA with the model (`--selected_rank`) +- Output can be written either to the model directory or a separated directory (`--out-dir`) +- In this project, for each dimer only one model is stored at [ModelArchive](https://modelarchive.org/) (MA) but the other models for the same dimer are stored in a Zip archive that goes into MA with the model (`--selected-rank`) - Following our [Docker README](../docker/README.md), the conversion can be called like this: ```terminal $ docker run --rm -v /home/user/models:/data -t converter:latest convert2modelcif --selected_rank 1 Q9Y5J9-Q9Y5L4/ diff --git a/projects/human-heterodimers-w-crosslinks/translate2modelcif.py b/projects/human-heterodimers-w-crosslinks/translate2modelcif.py index 4f5dbb70c4e25a5d7c4264c2e27a8a97b25833ab..a518deff9ab0e28af3b8dab3178c047545dc0ade 100755 --- a/projects/human-heterodimers-w-crosslinks/translate2modelcif.py +++ b/projects/human-heterodimers-w-crosslinks/translate2modelcif.py @@ -27,7 +27,7 @@ from ost import io # EXAMPLES for running: -# ost scripts/translate2modelcif.py --rank 1 --out_dir="./modelcif" \ +# ost scripts/translate2modelcif.py --selected-rank 1 --out-dir="./modelcif" \ # "A0A1B0GTU1-O75152" @@ -46,7 +46,7 @@ def _parse_args(): + "'<UniProtKB AC>-<UniProtKB AC>'", ) parser.add_argument( - "--selected_rank", + "--selected-rank", type=str, default=None, help="If a certain model of a modelling project is selected by rank, " @@ -54,7 +54,7 @@ def _parse_args(): + "accompanying files to the selected model.", ) parser.add_argument( - "--out_dir", + "--out-dir", type=str, metavar="<OUTPUT DIR>", default="",