update docs

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
+
+<iframe src="https://scribehow.com/embed/Add_Users_to_a_Nomad_Oasis_Upload__hGhkAMCATXWdHGjeleDB0A" width="100%" height="640" allowfullscreen frameborder="0"></iframe>
+
+## 2. Create a new sample entry
 <iframe src="https://scribehow.com/embed/Upload_custom_data_entry_with_specific_schema_in_NOMAD_Oasis__mRg47mlZSpOSQ5G_HFlq7A" width="100%" height="640" allowfullscreen frameborder="0"></iframe>
 
-## Add instrument entry
+## 3. Create sample processing conditions
+<iframe src="https://scribehow.com/embed/Create_Material_Processing_ELN_Entry_in_NOMAD_Oasis___8kJxxjiRueC6AIMpgGaAw" width="100%" height="640" allowfullscreen frameborder="0"></iframe>
+
+## 4. Add an instrument entry
 <iframe src="https://scribehow.com/embed/Create_a_Custom_Instrument_Schema_in_Nomad_Oasis__-RkLffMjT22hj9BAipE1KQ" width="100%" height="640" allowfullscreen frameborder="0"></iframe>
 
-## Add measurement entry
+## 5. Add a measurement entry
 
 <iframe src="https://scribehow.com/embed/Create_a_Measurement_Upload_in_NOMAD_Oasis__xqwktvKPQUSPK8aT0E-58A" width="100%" height="640" allowfullscreen frameborder="0"></iframe>
 
-## Upload gaussian DFT
+## 6. Upload a DFT calculation
 
 <iframe src="https://scribehow.com/embed/Upload_DFT_Files_Using_Nomad_Oasis_Interface__qdOffE1DSnSuvKsjP8dwZw" width="100%" height="640" allowfullscreen frameborder="0"></iframe>
 
-## Run a jupyter notebook to visualize the `.pdb` file
+## 7. Create an ExperimentELN entry
 
-<iframe src="https://scribehow.com/embed/Visualizing_pdb_files_through_NOMAD_Remote_Tools_Hub__IdryIk1lRpaDI8TQm6ajbg" width="100%" height="640" allowfullscreen frameborder="0"></iframe>
+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
 
-<iframe src="https://scribehow.com/embed/Add_Users_to_a_Nomad_Oasis_Upload__hGhkAMCATXWdHGjeleDB0A" width="100%" height="640" allowfullscreen frameborder="0"></iframe>
+<iframe src="https://scribehow.com/embed/Entry_Overview_and_Search_in_the_UniSysCatApp__NjapCJVCRpWOwL_diCv5eQ" width="100%" height="640" allowfullscreen frameborder="0"></iframe>
 
-## Use the dedicated UniSysCat Explore App to get an overview and find entries
+## 9. Run a jupyter notebook to visualize the `.pdb` file
+
+<iframe src="https://scribehow.com/embed/Visualizing_pdb_files_through_NOMAD_Remote_Tools_Hub__IdryIk1lRpaDI8TQm6ajbg" width="100%" height="640" allowfullscreen frameborder="0"></iframe>
 
-<iframe src="https://scribehow.com/embed/Entry_Overview_and_Search_in_the_UniSysCatApp__NjapCJVCRpWOwL_diCv5eQ" width="100%" height="640" allowfullscreen frameborder="0"></iframe>
+![gif for protein vizualization in jupyter hub](../images/Gif_protein_viz.gif)

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