diff --git a/docs/how_to/use_this_plugin.md b/docs/how_to/use_this_plugin.md index 24557c7..a30c280 100644 --- a/docs/how_to/use_this_plugin.md +++ b/docs/how_to/use_this_plugin.md @@ -4,28 +4,49 @@ This plugin can be used in a NOMAD Oasis installation. Check the tips in [Instal Once the NOMAD Oasis is deployed, you can generate different entries as shown below. -## Create new sample entries +## Outline +1. [Create an upload and manage users](#1-create-an-upload-and-manage-users) +2. [Create a new sample entry](#2-create-a-new-sample-entry) +3. [Create a sample processing conditions entry](#3-create-sample-processing-conditions) +4. [Add an instrument entry](#4-add-an-instrument-entry) +5. [Add a measurement entry](#5-add-a-measurement-entry) +6. [Upload a DFT calculation](#6-upload-a-dft-calculation) +7. [Create an ExperimentELN entry](#7-create-an-experimenteln-entry) +8. [Use the dedicated UniSysCat Explore App](#8-use-the-dedicated-unisyscat-explore-app-to-get-an-overview-and-find-entries) +9. [Run a jupyter notebook to visualize the `.pdb` file](#9-run-a-jupyter-notebook-to-visualize-the-pdb-file) + + +## 1. Create an upload and manage users + + + +## 2. Create a new sample entry -## Add instrument entry +## 3. Create sample processing conditions + + +## 4. Add an instrument entry -## Add measurement entry +## 5. Add a measurement entry -## Upload gaussian DFT +## 6. Upload a DFT calculation -## Run a jupyter notebook to visualize the `.pdb` file +## 7. Create an ExperimentELN entry - +You can create an Experiment entry and link all related activities in one entry, similar to the sample processing entry. Select ExperimentELN Entry from the drop-down menu and link the references in the subsection "steps" -## User management +## 8. Use the dedicated UniSysCat Explore App to get an overview and find entries - + -## Use the dedicated UniSysCat Explore App to get an overview and find entries +## 9. Run a jupyter notebook to visualize the `.pdb` file + + - \ No newline at end of file +![gif for protein vizualization in jupyter hub](../images/Gif_protein_viz.gif) \ No newline at end of file diff --git a/docs/images/Gif_protein_viz.gif b/docs/images/Gif_protein_viz.gif new file mode 100644 index 0000000..847e898 Binary files /dev/null and b/docs/images/Gif_protein_viz.gif differ diff --git a/src/nomad_unisyscat/schema_packages/mypackage.py b/src/nomad_unisyscat/schema_packages/mypackage.py index 7ad6c87..6058210 100644 --- a/src/nomad_unisyscat/schema_packages/mypackage.py +++ b/src/nomad_unisyscat/schema_packages/mypackage.py @@ -11,7 +11,6 @@ from nomad.datamodel.metainfo.basesections import ( CompositeSystem, CompositeSystemReference, - Instrument, InstrumentReference, Measurement, MeasurementResult, @@ -94,14 +93,6 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None: super().normalize(archive, logger) -class UniSysCatInstrument(Instrument, Schema): - m_def = Section( - label = 'Instrument entry', - categories=[UniSysCatElnCategory] - ) - - - class EPRSettings(ArchiveSection): metal_ions_defined = Quantity(type=bool) organic_radicals_defined = Quantity(type=bool) @@ -586,7 +577,7 @@ class IRSpectroscopy(Measurement, PlotSection, Schema): results.section_def = IRResult def normalize(self, archive, logger): - + super().normalize(archive, logger) if self.data_file is None: return