Merge pull request #74 from ghutchis/automated-contributors

Add "saving" to getting started as well as naming tutorial
Avogadro · Nov 28, 2023 · 7ec070c · 7ec070c
2 parents 80e6489 + b27b71c
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Showing 11 changed files with 29 additions and 9 deletions.
diff --git a/source/_static/Analysis-MoleculeProperties.png b/source/_static/Analysis-MoleculeProperties.png
diff --git a/source/_static/Ligand-CentroidMenu.png b/source/_static/Ligand-CentroidMenu.png
diff --git a/source/_static/NamingEthane.png b/source/_static/NamingEthane.png
diff --git a/source/_static/NamingSubstituted.png b/source/_static/NamingSubstituted.png
diff --git a/source/_static/OtherFunctionalGroup.png b/source/_static/OtherFunctionalGroup.png
diff --git a/source/_static/Template-LigandPerpendicular.png b/source/_static/Template-LigandPerpendicular.png
diff --git a/source/_static/tutorial-save.png b/source/_static/tutorial-save.png
diff --git a/source/docs/getting-started/index.md b/source/docs/getting-started/index.md
@@ -3,6 +3,7 @@
 * [Introduction](introduction)
 * [Drawing Molecules](drawing-molecules)
 * [Making Selections](making-selections)
+* [Saving Files](saving-files)
 
 ```{toctree}
 ---
@@ -13,4 +14,5 @@ hidden: true
 introduction
 drawing-molecules
 making-selections
+saving-files
 ```
diff --git a/source/docs/getting-started/saving-files.md b/source/docs/getting-started/saving-files.md
@@ -0,0 +1,20 @@
+# Saving Files
+
+By default, Avogadro saves files to "native" formats CJSON (Chemical JSON) and CML (Chemical Markup Language), which store as much chemical information as possible.
+
+![Screenshot indicating File => Save and Save As menu items](../../_static/tutorial-save.png)
+
+In particular the default [Chemical JSON](https://github.com/OpenChemistry/chemicaljson) format will retain atoms, bond orders, formal charges, unit cell parameters, space group information, surfaces, orbitals, vibrations and other spectra, selections, custom colors, etc.
+
+## Exporting to Other Formats
+
+If you wish to **export** to other formats (e.g., XYZ, PDB, SDF, etc.) use
+File => Export => Molecule…
+
+![Screenshot indicating File => Export => Molecule menu item](../../_static/FileExportMolecule.png)
+
+Avogadro uses support for [Open Babel](https://openbabel.org/) to write to over 100 different chemical file formats.
+
+```{tip} **New in 2.0**
+We separated the "export" to other formats into a new command because users would be surprised when saving to some formats (e.g., XYZ, PDB) and bond orders or other information would be lost.
+```
diff --git a/source/docs/index.md b/source/docs/index.md
@@ -1,8 +1,6 @@
 (Guide)=
 
-# User Guide
-
-## Avogadro: Molecular Editor and Visualization
+# Introduction
 
 Avogadro is a free, open source molecular editor and visualization tool, designed for use on Mac, Windows, and Linux in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.
 

diff --git a/source/docs/tutorials/naming-a-molecule.md b/source/docs/tutorials/naming-a-molecule.md
@@ -2,14 +2,14 @@
 
 Avogadro includes support for naming compounds using the PubChem database, which includes over 112 million compounds. Since these are deposited by chemical suppliers, pharmaceutical companies, etc. the database may not cover _**every**_ molecule you may build, but includes a broad selection of compounds.
 
-![](../../_static/media\_1340251460215.png)
+Open up the Molecule Properties window, under the Analysis menu.
 
-Open up the Molecule Properties window, under the View menu.
-
-![](../../_static/media\_1340251491638.png)
+![](../../_static/Analysis-MoleculeProperties.png)
 
 The IUPAC name will initially show as (pending) while the server returns the name, (unknown) if the molecule is not found in the resolver, or (unavailable) if your network connection is down or the resolver service is otherwise unreachable.
 
-![](../../_static/media\_1340251768869.png)
+![](../../_static/NamingEthane.png)
+
+As you modify the molecule (e.g., adding a Br atom or two), the name will update automatically with the other properties, albeit while temporarily showing (pending)
 
-As you modify the molecule (e.g., adding a Cl atom), the name will update automatically with the other properties, albeit while temporarily showing (pending)
+![](../../_static/NamingSubstituted.png)