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Commit 4e9dda3c authored by B13nch3n's avatar B13nch3n
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Explain remaining options

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...@@ -67,7 +67,7 @@ $ validate-mmcif-file -a extra model.cif ...@@ -67,7 +67,7 @@ $ validate-mmcif-file -a extra model.cif
$ $
``` ```
If the URL points to a subdirectory, that must be reflected by the associates directory declared to the validation tool. The following example illustrates that the `extra` directory needs a `pae` directory storing the associated file as expected by `_ma_entry_associated_files.file_url`: If the URL points to a subdirectory, this must be reflected by the associates directory tree declared to the validation tool. The following example illustrates that the `extra` directory needs a `pae` directory storing the associated file as expected by `_ma_entry_associated_files.file_url`:
```bash ```bash
$ grep _ma_entry_associated_files.file_url model.cif $ grep _ma_entry_associated_files.file_url model.cif
...@@ -81,10 +81,13 @@ $ validate-mmcif-file -a extra model.cif ...@@ -81,10 +81,13 @@ $ validate-mmcif-file -a extra model.cif
$ $
``` ```
### Misc. arguments
|**`--help`** (**`-h`**)|Print a help/ usage page for the validation tool.|
|**`--dict-sdb <SDB FILE>`** (**`-d`**)|Format dictionary in (binary) SDB format used for validating a ModelCIF file. The container comes with a SDB for ModelCIF and one for the original PDBx/mmCIF format.|
|**`--out-file <JSON FILE>`** (**`-o`**)|Instead of printing the output to `stdout`, store it in a JSON file.|
|**`--verbose`** (**`-v`**)|Write information from intermediate steps to `stdout`. This includes the raw output of `CifCheck`.|
- basic usage
- remaining options
## How to run the container ## How to run the container
...@@ -95,6 +98,6 @@ $ ...@@ -95,6 +98,6 @@ $
# Files in this directory # Files in this directory
<!-- LocalWords: PDBx ModelCIF TOC JSON CifCheck RCSB mmcif cif pdbx dic dir <!-- LocalWords: PDBx ModelCIF TOC JSON CifCheck RCSB mmcif cif pdbx dic dir
<!-- LocalWords: url pae <!-- LocalWords: url pae sdb SDB stdout
--> -->
--> -->
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