diff --git a/source/_static/Analysis-MoleculeProperties.png b/source/_static/Analysis-MoleculeProperties.png new file mode 100644 index 00000000..973cf725 Binary files /dev/null and b/source/_static/Analysis-MoleculeProperties.png differ diff --git a/source/_static/Ligand-CentroidMenu.png b/source/_static/Ligand-CentroidMenu.png index 5f481948..40d521d8 100644 Binary files a/source/_static/Ligand-CentroidMenu.png and b/source/_static/Ligand-CentroidMenu.png differ diff --git a/source/_static/NamingEthane.png b/source/_static/NamingEthane.png new file mode 100644 index 00000000..29626217 Binary files /dev/null and b/source/_static/NamingEthane.png differ diff --git a/source/_static/NamingSubstituted.png b/source/_static/NamingSubstituted.png new file mode 100644 index 00000000..064f8b44 Binary files /dev/null and b/source/_static/NamingSubstituted.png differ diff --git a/source/_static/OtherFunctionalGroup.png b/source/_static/OtherFunctionalGroup.png index 79d126bc..64ec9ebe 100644 Binary files a/source/_static/OtherFunctionalGroup.png and b/source/_static/OtherFunctionalGroup.png differ diff --git a/source/_static/Template-LigandPerpendicular.png b/source/_static/Template-LigandPerpendicular.png index e98b4c6d..81e41585 100644 Binary files a/source/_static/Template-LigandPerpendicular.png and b/source/_static/Template-LigandPerpendicular.png differ diff --git a/source/_static/tutorial-save.png b/source/_static/tutorial-save.png new file mode 100644 index 00000000..4eb3617e Binary files /dev/null and b/source/_static/tutorial-save.png differ diff --git a/source/docs/getting-started/index.md b/source/docs/getting-started/index.md index d03159d3..8e63e97c 100644 --- 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 new file mode 100644 index 00000000..581750be --- /dev/null +++ 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 index 68998c6e..ed33363b 100644 --- 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 index e13fe3cf..f3e5b220 100644 --- 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)