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a/_images/icon_bond-centric.svg b/_images/icon_bond-centric.svg new file mode 100644 index 00000000..388a698f --- /dev/null +++ b/_images/icon_bond-centric.svg @@ -0,0 +1,67 @@ + + + + diff --git a/_images/icon_draw.svg b/_images/icon_draw.svg new file mode 100644 index 00000000..b340646b --- /dev/null +++ b/_images/icon_draw.svg @@ -0,0 +1,40 @@ + + + + diff --git a/_images/icon_label.svg b/_images/icon_label.svg new file mode 100644 index 00000000..99567390 --- /dev/null +++ b/_images/icon_label.svg @@ -0,0 +1,40 @@ + + + + diff --git a/_images/icon_manipulate.svg b/_images/icon_manipulate.svg new file mode 100644 index 00000000..8cb9599b --- /dev/null +++ b/_images/icon_manipulate.svg @@ -0,0 +1,33 @@ + + + + diff --git a/_images/icon_measure.svg b/_images/icon_measure.svg new file mode 100644 index 00000000..03d5e1ee --- /dev/null +++ b/_images/icon_measure.svg @@ -0,0 +1,51 @@ + + + + diff --git a/_images/icon_navigate.svg b/_images/icon_navigate.svg new file mode 100644 index 00000000..27766909 --- /dev/null +++ b/_images/icon_navigate.svg @@ -0,0 +1,37 @@ + + + + diff --git a/_images/icon_select.svg b/_images/icon_select.svg new file mode 100644 index 00000000..6d55e58a --- /dev/null +++ b/_images/icon_select.svg @@ -0,0 +1,37 @@ + + + + diff --git a/_images/icon_template.svg b/_images/icon_template.svg new file mode 100644 index 00000000..a5f872d4 --- /dev/null +++ b/_images/icon_template.svg @@ -0,0 +1,82 @@ + + + + diff --git a/_images/toolbar_dark.svg b/_images/toolbar_dark.svg new file mode 100644 index 00000000..34390223 --- /dev/null +++ b/_images/toolbar_dark.svg @@ -0,0 +1,1704 @@ + + + + diff --git a/_sources/docs/getting-started/drawing-molecules.md.txt b/_sources/docs/getting-started/drawing-molecules.md.txt index 7153d544..7a601819 100644 --- a/_sources/docs/getting-started/drawing-molecules.md.txt +++ b/_sources/docs/getting-started/drawing-molecules.md.txt @@ -9,7 +9,7 @@ to attach functional groups or assemble inorganic and organometallic complexes. ![Screenshot of the draw tool](../../_static/draw-tool.png) -With the Draw Tool selected, left-clicking on the view frame will begin your journey into molecule creation. A left-click will create a carbon atom. A right-click on the atom will delete it. +With the Draw Tool selected, left-clicking on the view pane will begin your journey into molecule creation. A left-click will create a carbon atom. A right-click on the atom will delete it. ![](../../_static/first-carbon.png) @@ -21,7 +21,7 @@ Avogadro uses carbon as the default element. A different element can be selected ![](../../_static/pick-an-element.png) -Let's say you wanted to create water. You can either type in O, or select "Oxygen (8)" from the drop-down menu, and then click on the black view. +Let's say you wanted to create water. You can either type in O, or select "Oxygen (8)" from the drop-down menu, and then click on the (by default black) view pane. Left-clicking on an atom that has already been generated will also change the element. In this case, clicking on the initial carbon atom changed it into an oxygen atom. diff --git a/_sources/docs/getting-started/making-selections.md.txt b/_sources/docs/getting-started/making-selections.md.txt index 7d5a26d6..959cb489 100644 --- a/_sources/docs/getting-started/making-selections.md.txt +++ b/_sources/docs/getting-started/making-selections.md.txt @@ -6,7 +6,7 @@ The [Selection Tool](tools-selection-tool) is also a useful feature to master wh The Selection Tool provides you with the ability to select a single atom within a molecule. This is achieved by left-clicking the atom. Pressing and holding shift while clicking allows for the selection of multiple atoms. -Right-clicking on an empty part of the view will clear the selection made. +Right-clicking on an empty part of the view pane will clear the selection made. ```{warning} A known bug means that on some systems, multiple left-clicks are required to clear the selection. diff --git a/_sources/docs/getting-started/saving-files.md.txt b/_sources/docs/getting-started/saving-files.md.txt index 3d14c177..f8dd55cc 100644 --- a/_sources/docs/getting-started/saving-files.md.txt +++ b/_sources/docs/getting-started/saving-files.md.txt @@ -11,7 +11,7 @@ CML (Chemical Markup Language) was the original save format for Avogadro and sup ## Exporting to other formats If you wish to **export** to other formats (e.g., XYZ, PDB, SDF, etc.) use -`File` ⇒ `Export` ⇒ `Molecule…` +`File`⇒`Export`⇒`Molecule…` ![Screenshot indicating File => Export => Molecule menu item](../../_static/FileExportMolecule.png) diff --git a/_sources/docs/index.md.txt b/_sources/docs/index.md.txt index 55e526da..0998c7fa 100644 --- a/_sources/docs/index.md.txt +++ b/_sources/docs/index.md.txt @@ -12,7 +12,7 @@ Avogadro is designed for cross-platform use and is fully supported on Windows, L ## Avogadro 2 -In particular, this manual covers the new release of Avogadro 2, a major update, and includes major changes, the revised interface, and new features. +In particular, this manual covers the new release of Avogadro 2, a major update, and includes major changes, a revised interface, and new features. Most sections include notes on changes from v1.0, 1.1, and 1.2 to the new 2.0 release, though as there have been so many, coverage is not in any way comprehensive. Versions 1.90 to 1.99 were beta releases of Avogadro 2 and a lot of this manual applied to those versions too, but note that during the beta phase there were also many improvements made to the UI which have changed the location or appearance of various things. @@ -20,6 +20,7 @@ Versions 1.90 to 1.99 were beta releases of Avogadro 2 and a lot of this manual Look out for boxes highlighting new features or changes for Avogadro 2: :::{versionadded} 2.0 +This feature is new. ::: :::{versionchanged} 2.0 @@ -49,7 +50,7 @@ Initial funding for the Avogadro manual was provided by the [University of Pitts * Version 1 - Summer 2015 - Taylor Cornell and Geoffrey Hutchison * Version 2 - 2022-2024 - Geoffrey Hutchison and Matt Milner -```{toctree} +:::{toctree} --- hidden: true caption: User Documentation @@ -66,4 +67,4 @@ optimizing-geometry/index display-types/index extensions/index tutorials/index -``` +::: diff --git a/_sources/docs/menus/build-menu.md.txt b/_sources/docs/menus/build-menu.md.txt index 4cbf10de..247841f9 100644 --- a/_sources/docs/menus/build-menu.md.txt +++ b/_sources/docs/menus/build-menu.md.txt @@ -57,6 +57,7 @@ The displayed data can also be modified according to your personal preference, o ![](../../_static/remove-hydrogens.png) ## Insert +(menus-build-menu-insert)= "Insert" provides a faster, simpler way of building molecules. A depicted below, you can insert DNA/RNA, a Fragment, a Peptide, and can also insert a molecule based on SMILES text. diff --git a/_sources/docs/panes/index.md.txt b/_sources/docs/panes/index.md.txt index 19802eb2..5fa3d68d 100644 --- a/_sources/docs/panes/index.md.txt +++ b/_sources/docs/panes/index.md.txt @@ -1,2 +1,2 @@ -(panels)= +(panes)= diff --git a/_sources/docs/panes/properties.md.txt b/_sources/docs/panes/properties.md.txt new file mode 100644 index 00000000..2671e842 --- /dev/null +++ b/_sources/docs/panes/properties.md.txt @@ -0,0 +1,13 @@ +(panes-properties)= + +(panes-properties-molecular)= + +(panes-properties-atom)= + +(panes-properties-bond)= + +(panes-properties-angle)= + +(panes-properties-torsion)= + +(panes-properties-residue)= \ No newline at end of file diff --git a/_sources/docs/panes/view-configuration.md.txt b/_sources/docs/panes/view.md.txt similarity index 100% rename from _sources/docs/panes/view-configuration.md.txt rename to _sources/docs/panes/view.md.txt diff --git a/_sources/docs/settings/language.md.txt b/_sources/docs/settings/language.md.txt index 3eed8628..149a0270 100644 --- a/_sources/docs/settings/language.md.txt +++ b/_sources/docs/settings/language.md.txt @@ -2,7 +2,7 @@ # Language -By default Avogadro will use your system language, but you can change this by going to `Extensions` ⇒ `User Interface Language…`. +By default Avogadro will use your system language, but you can change this by going to `Extensions`⇒`User Interface Language…`. Avogadro is available in many languages. Languages with significant coverage as of v1.99 include English (US, GB, AU, CA), Chinese, Esperanto, French, Georgian, German, Hungarian, Japanese, Korean, Portuguese (PT, BR), Serbian, Spanish, and Turkish. Many others have partial coverage and are in progress all the time! diff --git a/_sources/docs/tools/align-tool.md.txt b/_sources/docs/tools/align-tool.md.txt index e284e6b5..96772494 100644 --- a/_sources/docs/tools/align-tool.md.txt +++ b/_sources/docs/tools/align-tool.md.txt @@ -8,9 +8,11 @@ The Align Tool is used to rotate and translate a molecule(s) so that it aligns w ## Basic usage -First, an alignment axis is chosen from the `Axis` drop-down menu in the Align Pane. The x, y, and z keys on the keyboard are shortcuts for changing the alignment axis. +First, an alignment axis is chosen from the `Axis` drop-down menu in the Align Pane. +The x, y, and z keys on the keyboard are shortcuts for changing the alignment axis. -Secondly, select either one or two atoms in the view frame with the left mouse button. The labels #1 and #2 will be displayed on each. +Secondly, select either one or two atoms in the view frame with the left mouse button. +The labels #1 and #2 will be displayed on each. Clicking `Align` will then reposition the molecule as desired. @@ -30,7 +32,8 @@ The `Axis` drop-down menu allows you to choose which Cartesian axis the molecule ![](../../_static/ec6c967d-5df0-41b8-b692-93123f8a0462.png) -By default, the relative positions of everything in the view frame will remain the same and the same transformation will be applied to all objects. By choosing the "Molecule" option in the `Align` drop-down menu in the Align Pane, only the molecule containing the selected atoms will be affected by the change. +By default, the relative positions of everything in the view frame will remain the same and the same transformation will be applied to all objects. +By choosing the "Molecule" option in the `Align` drop-down menu in the Align Pane, only the molecule containing the selected atoms will be affected by the change. ![](../../_static/c1839173-f147-444d-b9c9-9ebb2e0a28f4.png) diff --git a/_sources/docs/tools/animation-tool.md.txt b/_sources/docs/tools/animation-tool.md.txt index 3e9e4036..45b316ad 100644 --- a/_sources/docs/tools/animation-tool.md.txt +++ b/_sources/docs/tools/animation-tool.md.txt @@ -2,4 +2,6 @@ # Animation Tool -![The icon of the Animation Tool in light mode.](../../_static/icon_player.svg) \ No newline at end of file +![The icon of the Animation Tool in light mode.](../../_static/icon_player.svg) + +Keyboard shortcut: Ctrl+9 \ No newline at end of file diff --git a/_sources/docs/tools/auto-rotate-tool.md.txt b/_sources/docs/tools/auto-rotate-tool.md.txt index add18409..d1ae02b7 100644 --- a/_sources/docs/tools/auto-rotate-tool.md.txt +++ b/_sources/docs/tools/auto-rotate-tool.md.txt @@ -4,7 +4,8 @@ The auto rotate tool allows for the continuous rotation of a molecule. ![](../../_static/bcfbd92f-d657-492e-8a93-1332a59ada97.png) -To rotate the molecule, adjust the x, y, and z rotation scales as desired. Then select "Start". +To rotate the molecule, adjust the x, y, and z rotation scales as desired. +Then select "Start". ![](../../_static/a328868b-9edd-452d-b6db-81f8f8e70343.png) diff --git a/_sources/docs/tools/bond-centric-manipulation-tool.md.txt b/_sources/docs/tools/bond-centric-manipulation-tool.md.txt index 4be762bb..ee688752 100644 --- a/_sources/docs/tools/bond-centric-manipulation-tool.md.txt +++ b/_sources/docs/tools/bond-centric-manipulation-tool.md.txt @@ -2,8 +2,17 @@ # Bond-Centric Manipulation Tool +![The icon of the Bond-Centric Manipulation Tool in light mode.](../../_static/icon_bond-centric.svg) + +Keyboard shortcut: Ctrl+7 + The Bond-Centric Manipulation Tool is a powerful tool that allows you to focus on a specific bond and change its length and the surrounding angles, while keeping the rest of the molecule the same. +```{tip} +The Bond-Centric Manipulation Tool provides mouse-based manual adjustment of bond lengths and angles. +If you wish to set these quantities to specific, exact values, it may be more convenient to do this in the relevant [Properties pane](panes-properties). +``` + ![](../../_static/bb1e744d-c5be-45b9-a6ce-b3de75ae47e2.png) ## Starting with the basics: diff --git a/_sources/docs/tools/draw-tool.md.txt b/_sources/docs/tools/draw-tool.md.txt index 16f7b25b..7bb33cc4 100644 --- a/_sources/docs/tools/draw-tool.md.txt +++ b/_sources/docs/tools/draw-tool.md.txt @@ -2,52 +2,96 @@ # Draw Tool -Molecules are built and edited with the Draw Tool, which allows "free-hand" sketching of new molecules. +![The icon of the Draw Tool in light mode.](../../_static/icon_draw.svg) -```{tip} **New in 2.0** -You can also use the new [Template Tool](template-tool), which makes it quicker and easier to attach functional groups or assemble inorganic/organometallic complexes. -``` +Keyboard shortcut: Ctrl+2 -![Screenshot of the draw tool](../../_static/draw-tool.png) +Molecules are **built** and **edited** with the **Draw Tool**, which allows "free-hand" sketching of new molecules. -Left-clicking on the display will allow you to begin your journey into molecule creation. A left-click will create a carbon atom. A right-click will delete the atom. +:::{tip} +To help rapidly build your structure you can also use the new [Template Tool](tools-template-tool), which makes it quicker and easier to attach functional groups or assemble inorganic/organometallic complexes. +::: -![](../../_static/first-carbon.png) +:::{versionadded} 2.0 +The default bond order setting is now **Automatic** -- it will adjust intelligently with the length of the bond. +::: -Left-clicking the initial atom and dragging your mouse will create a bond to another carbon atom. +## Basic usage -![](../../_static/drag-to-build.png) +Atoms and bonds are drawn using the mouse. -Avogadro uses carbon as the default element. A different element can be selected through the `Element` drop-down menu. Typing the atomic symbol (e.g., O for Oxygen, As for Arsenic) is a shortcut for changing the selected element. +Left-click on an **empty space** in the view pane to **create an atom** of the currently selected element. -![](../../_static/pick-an-element.png) +Left-click on an **existing atom** to **change its element** to the one currently selected. -Let's say you wanted to create water. You can either type in "O", or select "Oxygen (8)" from the drop-down menu, and then click on the black display. +**Left-click and drag** from an atom to **create a new bond** starting from that atom. +A new atom of the currently selected element is automatically created at the end of the new bond and is visible while dragging. -Left-clicking on an atom that has already been generated will also change the element. In this case, clicking on the initial carbon atom changed it into an oxygen atom. +:::{tip} +New atoms and bonds will be created in a plane that is parallel to the screen and includes the atom the bond originates from. +::: -![](../../_static/tutorial-water.png) +If, during the drag, the mouse is moved over an existing atom, the mouse will "snap" to it, and the new atom will disappear. +The new bond will be drawn to this existing atom instead. -If the `Adjust Hydrogens` box is checked, hydrogen atoms in the molecule will be automatically adjusted to satisfy valency (as shown above). +By default, the bond order of a new bond is selected automatically based on the distance between the atoms: long bonds will be single bonds, short bonds will be double bonds, and very short bonds will be triple bonds. -![](../../_static/tutorial-adjust-hydrogens.png) +Left-click on an **existing bond** to **increase its bond order** by one. +Left-clicking on a triple bond turns it back into a single bond. -Bond order is changed through the `Bond Order` drop-down menu, or by typing the numbers 1, 2, or 3. Bonds are added by left-clicking on a bond that has already been created. Right-clicking on a bond deletes the bond. +**Delete** atoms and bonds by **right-clicking** on them. -![](../../_static/tutorial-bond-order.png) +## Pane options -```{tip} **New in 2.0** -The default bond order is "Automatic," and will adjust with the length of the bond. -``` +Element +: Choose the element of new atoms. -### Creating Carbon Dioxide + Various common elements are shown in the drop-down for easy access, but any element can be selected from the periodic table by choosing **Other…**. + Used elements are remembered and will appear in the drop-down in future. -Begin drawing the "O-C-O" structure. After the structure is drawn, all you need to do is left-click on the bonds. Left-clicking on the bonds will create a double bond (shown below). + Alternatively, use the handy keyboard shortcuts -- just type the atomic symbol of the desired element (e.g., O for Oxygen, As for Arsenic). -![](../../_static/tutorial-co2-step1.png) -![](../../_static/tutorial-co2-step2.png) -![](../../_static/tutorial-co2-step3.png) +Bond Order +: Choose the bond order of new bonds. -Once you've created your molecule, you can optimize its geometry through the `Extensions` menu. Selecting the `Extensions` menu, and clicking `Optimize Geometry` will provide your molecule with proper bond lengths and angles. + There are keyboard shortcuts for this too -- 1 selects single, 2 double, and so on. -![](../../_static/ada26872-ede7-4601-bd4e-d790c10ad614.png) + When the bond order setting is set to **Automatic** (default), new bonds are given a bond order based on their length. + The cut-offs are determined by the elements of the atoms at either end of the bond. + + :::{tip} + Single bonds are created when the bond length exceeds the sum of the atoms' covalent radii. + Double bonds are created when the bond length is between 91% and 100% of the sum of the covalent radii, and anything shorter than 91% becomes a triple bond. + + For a carbon-carbon bond, the lower cut-offs are thus approx. 1.52 Å for a single bond and 1.38 Å for a double. + ::: + +Adjust Hydrogens +: Toggle automatically addition and removal of hydrogen atoms to fill valencies. + + If this box is checked (default), extra hydrogen atoms will be automatically added to new atoms to satisfy their valency. + When a bond is created or the order of a bond is changed, the number of hydrogen atoms on the atoms at each end of the bond will also be adjusted. + + For main-group elements, the default valency is always that predicted by the octet rule, while metal atoms are always created alone, without bonded atoms. + To create metal centers or hypervalent main-group centers, it is often better to use the [Template Tool](tools-template-tool). + + :::{warning} + It may not be possible to deliberately add or remove hydrogen atoms (for example, to create a radical or an ion) while this setting is checked. + + If this is desired, turn off the setting while manually adjusting the hydrogens. + Turning the setting back on will not cause the number of hydrogen atoms to be readjusted. + ::: + +## Adjusting the structure + +It is challenging to draw structures in 3D on a 2D screen. +Using the Draw Tool alone will probably not give you a molecule that looks sensible and is representative of the real geometry. + +For manual adjustment, the position of the atoms can be fine-tuned by using the [Manipulation Tool](tools-manipulation-tool) in combination with the [Navigation Tool](tools-navigation-tool) to rotate and pan the view. + +To quickly get a sensible geometry, make use of the [`Optimize Geometry`](calculations-optimization) extension. +This can be conveniently activated using the shortcut Ctrl+Alt+O. + +## Tutorial + +A step-by-step tutorial for some simple molecules can be found [here](tutorials-drawing-simple-molecules). \ No newline at end of file diff --git a/_sources/docs/tools/index.md.txt b/_sources/docs/tools/index.md.txt index 1d53f116..fd33b691 100644 --- a/_sources/docs/tools/index.md.txt +++ b/_sources/docs/tools/index.md.txt @@ -4,11 +4,17 @@ Each tool in Avogadro has an associated icon in the toolbar: -![Toolbar](../../_static/toolbar_dark.svg) +![The appearance of the toolbar in dark mode.](../../_static/toolbar_dark.svg) -Hovering over a tool with the mouse gives a brief description of how to use it. +Within Avogadro, hovering over a tool icon with the mouse gives a brief description of how to use it. -After selecting a tool, the name of the tool and any options available for the tool are displayed in the [Tool Pane](panes-tool-pane). +Tools can be selected either by left-clicking the icon, or using the keyboard by pressing Ctrl and the corresponding number key (1 through 9 and 0, left to right). + +After selecting a tool, the name of the tool and any options available for the tool are displayed to the left in the [Tool pane](panes-tool-pane). + +:::{versionadded} 2.0 +The [Template Tool](tools-template-tool), [Label Tool](tools-label-tool) and [Animation Tool](tools-animation-tool) are all completely new tools. +::: ```{toctree} --- diff --git a/_sources/docs/tools/label-tool.md.txt b/_sources/docs/tools/label-tool.md.txt new file mode 100644 index 00000000..06f0e85b --- /dev/null +++ b/_sources/docs/tools/label-tool.md.txt @@ -0,0 +1,37 @@ +(tools-label-tool)= + +# Label Tool + +![The icon of the Label Tool in light mode.](../../_static/icon_label.svg) + +Keyboard shortcut: Ctrl+3 + +The **Label Tool** is used to **add custom text** to atoms. + +## Basic usage + +**Left-click** on an atom to **create a new label**. +A cursor will appear. + +Type the desired label with the keyboard. + +Press Enter or click anywhere else in the view pane to confirm the new label. + +:::{warning} +By default, atom labels are not visible in Avogadro! + +To show labels, enable the `Labels` display type in the [Display Types pane](panes-display-types). Open the options for the `Labels` display type by clicking the three bullets **⋯** + +Then, to show the custom labels, in the `Atom Label` drop-down of the Display Type Configuration pane, change the selected label type to **Custom**. +::: + +Edit an existing label by left-clicking on it. +Its position will raise slightly to indicate that it is being edited. + +## Pane options + +There are currently no options for this tool in the Edit Labels pane. + +The Label Tool is a work in progress and the ability to customize individual labels will likely come in future releases. + +Display settings for *all* labels, such as text color and placement, can be changed in the [Display Type Configuration pane](panes-display-types-labels) for the `Labels` display type. \ No newline at end of file diff --git a/_sources/docs/tools/manipulation-tool.md.txt b/_sources/docs/tools/manipulation-tool.md.txt index 908c591a..ffbb45f1 100644 --- a/_sources/docs/tools/manipulation-tool.md.txt +++ b/_sources/docs/tools/manipulation-tool.md.txt @@ -2,42 +2,67 @@ # Manipulation Tool -The Manipulation Tool allows you to move individual atoms as well as fragments. +![The icon of the Manipulation Tool in light mode.](../../_static/icon_manipulate.svg) -![](../../_static/520ebec1-6470-4f93-af26-c94ac5ea6f9d.png) +Keyboard shortcut: Ctrl+6 -If one or more atoms have been selected with the [Selection Tool](tools-selection-tool), all operations will be carried out on the entire selection as one unit. If nothing has been selected, whichever atom is dragged will be moved. +The **Manipulation Tool** allows you to **move** atoms, molecules, and fragments. ## Basic usage -Atoms can be translated by clicking and dragging with the left mouse button. +**Click and drag** an atom to **manipulate** it. + +The Manipulation Tool operates in two different modes: + +1. If one or more atoms have been selected, for example with the [Selection Tool](tools-selection-tool), all transformations will be carried out on the entire current selection as one unit. + +2. If nothing has been selected, whichever atom is clicked will be moved. + +**Translate atoms** or fragments by clicking and dragging them with the **left mouse button**. ```{tip} -When translating with click and drag, atoms will always move parallel to the screen; their depth will not change. For effective positioning within 3D space, it is thus necessary to combine the Manipulation Tool with the Navigation Tool to rotate the molecule. +When translating with click and drag, atoms will always move parallel to the screen; their depth will not change. +For effective positioning within 3D space, it is thus necessary to combine the Manipulation Tool with the Navigation Tool to rotate the molecule. ``` -Atoms can be rotated by clicking and dragging with the right mouse button. +**Rotate atoms** or fragments by clicking and dragging them with the **right mouse button**. +On a single atom this will have no visible effect. ```{tip} Rotation with click and drag will always be about the geometric center of the selection. ``` -The Manipulation Tool is automatically selected after inserting a fragment, to enable quick and easy positioning of the new fragment. +The Manipulation Tool is automatically selected after [inserting a fragment](menus-build-menu-insert) via `Build`⇒`Insert`, to enable quick and easy positioning of the new fragment. ## Pane options The options in the Manipulate Pane allow you to apply transformations mathematically to the currently selected atoms. -Shifts along the X-, Y-, and Z-axes can be specified in angstrom. +Translate by: +: Specify the distances, in angstrom, to shift the selection along the X-, Y-, and Z-axes. + +![Applying a mathematical translation.](../../_static/0f89679e-9bee-4005-8793-fc96682ecd34.png){height=300px align=center} + +Rotate around: +: Specify the angles, in degrees, to rotate the selection around the X-, Y-, and Z-axes, as well as the centre of the rotation. + + The rotation can be carried out around the center of the current geometry or the origin, selected from the drop-down menu. + The X-, Y-, and Z-axes used for the rotation will be considered to intersect at this point. + +![Applying a mathematical rotation.](../../_static/14c1bee4-7288-4fa7-8660-d9fc58578631.png){height=300px align=center} -![](../../_static/0f89679e-9bee-4005-8793-fc96682ecd34.png) +Apply +: Apply the specified transformations to the current selection. -The "Rotate around:" section allows you to rotate your selection around the current geometry, or the origin. After choosing how many degrees to rotate your selection click "Apply". + If values for both translation and rotation have been entered, both will be applied. -![](../../_static/14c1bee4-7288-4fa7-8660-d9fc58578631.png) +Reset +: Reset all values in the translation and rotation boxes to 0. -Clicking "Reset" will reset all information in the translation, and rotation boxes. This does not reset the molecule, if you want to undo your adjustments go to the "Edit" menu in the top bar and select "Undo Manipulate Atom". + This does not reset the molecule or reverse any transformations; if you want to undo your adjustments, go to the `Edit` menu in the top bar and select `Undo Manipulate Atom`. -![](../../_static/e711ffa1-6a52-4748-af42-e734581bf36b.png) +![Undoing transformations.](../../_static/e711ffa1-6a52-4748-af42-e734581bf36b.png){height=600px align=center} -The icon for the Manipulation Tool is adapted from a design by [Ryan Dell](https://thenounproject.com/ryandeel/), a contributor to the Noun Project. \ No newline at end of file +:::{note} +The icon for the Manipulation Tool is adapted from a design by [Ryan Dell](https://thenounproject.com/ryandeel/), a contributor to the Noun Project. +::: \ No newline at end of file diff --git a/_sources/docs/tools/measure-tool.md.txt b/_sources/docs/tools/measure-tool.md.txt index 303eb0c5..de0e64a7 100644 --- a/_sources/docs/tools/measure-tool.md.txt +++ b/_sources/docs/tools/measure-tool.md.txt @@ -1,5 +1,9 @@ # Measure Tool +![The icon of the Measure Tool in light mode.](../../_static/icon_measure.svg) + +Keyboard shortcut: Ctrl+8 + The measure tool determines bond lengths, angles, and dihedrals. ![](../../_static/0b676e91-6deb-4eaa-8b5f-46774243643b.png) @@ -8,11 +12,13 @@ The measure tool allows you to select and assess up to four atoms. ![](../../_static/f0834455-f16b-4392-8ff4-5bf434c1dd63.png) -As you click on atoms Avogadro will automatically calculate the distances between atoms in a respective order. For example, the distance between atom 1 and 2 is 1.376 Å \(displayed below\). +As you click on atoms Avogadro will automatically calculate the distances between atoms in a respective order. +For example, the distance between atom 1 and 2 is 1.376 Å \(displayed below\). ![](../../_static/6adb2241-2518-4a8e-a015-cbb087d4b0f1.png) -Avogadro will also determine the angle between atoms, if at least three atoms have been selected. The second atom is used as the vertex. +Avogadro will also determine the angle between atoms, if at least three atoms have been selected. +The second atom is used as the vertex. ![](../../_static/6adb2241-2518-4a8e-a015-cbb087d4b0f1-1.png) diff --git a/_sources/docs/tools/navigation-tool.md.txt b/_sources/docs/tools/navigation-tool.md.txt index d6f00f6a..50afb143 100644 --- a/_sources/docs/tools/navigation-tool.md.txt +++ b/_sources/docs/tools/navigation-tool.md.txt @@ -1,26 +1,43 @@ +(tools-navigation-tool)= + # Navigation Tool -The Navigation Tool is used to pan, rotate, and scale the view of a molecule. +![The icon of the Navigation Tool in light mode.](../../_static/icon_navigate.svg) + +Keyboard shortcut: Ctrl+1 + +The **Navigation Tool** is used to **rotate**, **pan**, and **zoom** the view of a molecule within the view pane. + +Only the perspective of the view is changed, and the positions in space of all atoms are preserved. +To move atoms, fragments, or molecules within 3D space, use the [Manipulation Tool](tools-manipulation-tool) instead. -![](../../_static/ae875d6f-8727-4046-a615-d05606267865.png) +:::{tip} +When using any of the other tools, if a mouse or keyboard action is not defined for that tool but it is defined for the Navigation Tool, the action will have the same effect as if the Navigation Tool was selected. -If the "Display visual cues" box is checked, yellow arrows will display what type of navigation is taking place. +This means that many of the below actions will also work from some other tools. +For example, left-click and drag will also rotate the view while the [Animation Tool](tools-animation-tool) is selected. +::: -![](../../_static/1d3f24d3-2090-459b-9c21-a68840c203b1.png) +## Basic usage -Clicking anywhere on the black display and dragging the mouse will tilt, and rotate the entire molecule \(as shown below\). +**Rotate** the view by clicking and dragging anywhere on the view pane with the **left mouse button**. -![](../../_static/5bdfcdc2-53a3-43e0-a35a-3f157a685ed8.png) +Moving the mouse in a particular direction will rotate the view such that the part of the molecule nearest to you moves in the same direction. +For example, clicking and dragging to the left will cause the molecule to rotate clockwise (as considered looking from the top down). -A molecule can also be rotated about an atom by clicking the atom and dragging the mouse. Depicted below, acetone is being rotated about its initial carbon. +:::{tip} +Rotation with click and drag will always be about the geometric center of the molecule. +::: -![](../../_static/56ffe995-b194-4fe3-9f9c-21bf24c7c6e9.png) +**Pan** the view can be panned by clicking and dragging with the **right mouse button**. -Right clicking allows you to change the molecules location on the display. Double clicking the molecule will reset the molecule's view. +Again, when panning, the molecule will move in the direction the mouse is moved in. -![](../../_static/51e78183-938b-4c4e-a422-fc72d2a16876.png) +The **zoom level** can be increased and decreased using the **mouse scroll wheel**. -Using the middle scroll bar on a mouse will allow you to zoom in and out. +## Pane options -![](../../_static/2e656d2b-c082-4edf-8dc2-bafbe8a11834.png) +Reverse Direction of Zoom on Scroll +: Toggle the direction that is zoomed when scrolled. + Note that the default behavior is determined by your operating system's settings. diff --git a/_sources/docs/tools/selection-tool.md.txt b/_sources/docs/tools/selection-tool.md.txt index 37ae3874..f81b0db3 100644 --- a/_sources/docs/tools/selection-tool.md.txt +++ b/_sources/docs/tools/selection-tool.md.txt @@ -2,22 +2,72 @@ # Selection Tool -The selection tool allows the individual selection of atoms, bonds, or fragments. +![The icon of the Selection Tool in light mode.](../../_static/icon_select.svg) -![](../../_static/tutorial-select-tool.png) +Keyboard shortcut: Ctrl+5 -The select provides you with the ability to select a single atom within a molecule. This is achieved by left clicking the atom. Press and holding the "shift" key allows for the selection of multiple atoms. +The **Selection Tool** is used to **select atoms** with the mouse, either by individually picking them out or using a marquee selection box. -Right clicking on the black display will clear the selection made. +:::{tip} +Further useful selection functionality is available in the [`Select` menu](menus-select-menu). +::: -![](../../_static/tutorial-select-atom.png) +## Basic usage -You can also double-click on an atom to select all atoms connected in that fragment or molecule. +**Left-click** on an individual atom to **select** it. -![](../../_static/tutorial-select-all.png) +![A single atom selected after clicking on it.](../../_static/tutorial-select-atom.png){height=300px align=center} -Clicking and dragging your cursor is another way molecules, or fragments of molecules can be selected. +**Left-click and drag** to **select multiple** atoms by drawing a marquee selection box that covers the desired selection. -![](../../_static/tutorial-select-drag.png) +![A selection box as visible while dragging.](../../_static/tutorial-select-drag.png){height=300px align=center} -More information on selections can be found in the ["Select" menu](select-menu). +**Double-left-click** on an atom to instantly **select all connected atoms**. +"Connected" atoms are any that can be traced to the clicked atom through bonds, including over multiple bonds i.e. the whole molecule. + +![An entire molecule selected after clicking on one of its constituent atoms.](../../_static/tutorial-select-all.png){height=300px align=center} + +:::{tip} +Use `Select`⇒`Enlarge Selection` to increase the selection from an atom to only its immediate neighbors rather than the whole molecule. +::: + +Holding Shift or Ctrl while doing the above actions modifies their behaviour. + +The effects of the modifier keys are best summarized in the table below: + +| | with no modifier | with Shift | with Ctrl | +| --- | --- | --- | --- | +| *general effect* | *select* | *add* | *toggle/invert* | +| **click** | Atom is selected. | Atom is added to selection. | Atom is toggled between selected and unselected. | +| **click and drag** | All atoms within box are selected. | All atoms within box are added to selection. | Unselected atoms within box are selected, but selected atoms are deselected. | +| **double-click** | Whole molecule is selected. | Whole molecule is added to selection. | Unselected atoms within the molecule are selected, but selected atoms are deselected. | +| *effect on other atoms* | Other atoms are deselected. | All previously selected atoms remain selected. | Other atoms remain as they were. | + +Note that while Ctrl and **double-left-click** inverts the selection, this only affects **connected atoms**, whereas when `Select`⇒`Invert Selection` is used, the inversion applies to all atoms. + +**Select all atoms** using the keyboard shortcut Ctrl+A. + +**Clear the selection** by **right-clicking** in an empty part of the view pane or using the keyboard shortcut Ctrl+Shift+A. + +:::{tip} +The keyboard shortcuts for select/deselect all are always available, not only when the Selection Tool is the currently selected tool. +::: + +:::{warning} +A known bug means that right-clicking to clear the selection does not work on some systems. A triple-left-click on empty space or a left-click on any currently selected atom should do the trick instead. +::: + +## Pane options + +Apply Color +: Pick a color and apply it to the currently selected atoms. + + Clicking the colored rectangle will open a color picker. + After choosing a color, click `OK` to apply it. + +Change Layer +: Move the selected atoms to a different layer. + + Putting parts of a molecule, or members of an ensemble, into different layers allows different visual settings to be applied to different elements within the same ["Molecule"](panes-molecules) (what Avogadro calls a file). + + See [Layers](panes-layers) for more information on how to use them. diff --git a/_sources/docs/tools/template-tool.md.txt b/_sources/docs/tools/template-tool.md.txt index e5176ee4..90a81ec3 100644 --- a/_sources/docs/tools/template-tool.md.txt +++ b/_sources/docs/tools/template-tool.md.txt @@ -1,97 +1,177 @@ -(template-tool)= +(tools-template-tool)= # Template Tool -The template tool makes it easy to build up molecules from pre-defined ligands or functional groups, for example metal complexes or organometallic species. +![The icon of the Template Tool in light mode.](../../_static/icon_template.svg) -![Template tool window indicating menus for element, formal charge, and coordination geometry](../../_static/Template-CenterDialog.png) +Keyboard shortcut: Ctrl+3 -## Inserting Atoms with Specific Geometry +With the **Template Tool**, a variety of **pre-built fragments** can be created. -The "Element" menu includes many common transition metals as well as carbon, phosphorous and sulfur, as well as "Other…" which brings up a periodic table to select any element. +The Template Tool makes it easy to build up metal complexes or organometallic species from pre-defined coordination centers and ligands. -![Menu of elements, including carbon, phosphorus, sulfur, and transition metals](../../_static/Template-Element.png) +The Template Tool also enables rapid addition of functional groups to an organic framework. -The "Formal Charge" menu allows you to specify a formal charge on the atom, which is used to calculate the total molecular charge for a calculation or force field optimization. +:::{versionadded} 2.0 +::: -The "Coordination" menu allows you to specify the number of attachment points and geometry of the atom, including common arrangements from one to eight ligands. This includes linear, trigonal planar, tetrahedral, square planar, trigonal bipyramidal, octahedral, as well as less common geometries such as square pyramidal, trigonal prism, pentagonal bipyramidal, and square antiprism. +## Basic usage -![Menu of coordination geometries including linear, trigonal planar, tetrahedral, square planar, trigonal bipyramidal, and octahedral](../../_static/Template-Coordination.png) +Ligands and functional groups must be added to an existing atom (a "center"), whether this be an atom within an organic framework or a metal center. -After selecting a coordination type from the menu, the preview will update to reflect the geometry. +Elements in the third period and below can often exhibit multiple different coordination geometries, which are not easily created using the [Draw Tool](tools-draw-tool). +To achieve these, use the **"Centers"** templates. -Once you have selected the element, formal charge (if desired), and coordination, click in the scene to insert the atom. +A center of any element and with any common coordination geometry can be selected from the `Center` tab of the Template pane. +**Left-click** on an **empty space** in the view pane to **create a center** with attached hydrogens at each coordination site. -![Image of octahedral iron atom with six white hydrogen atoms](../../_static/OctIron.png) +![Image of octahedral iron atom with six white hydrogen atoms.](../../_static/OctIron.png){height=300px align=center} -## Attaching Ligands +Once at least one center is present, ligands or functional groups can be added. +The desired ligand or group can be selected from the respective tabs of the Template pane. +**Left-click any hydrogen atom** in the view pane to replace it with the ligand or functional group, with the attachment point as shown in the preview image. -The second tab in the template tool window allows you to select from a range of ligand types, including common [bidentate](https://en.wikipedia.org/wiki/Denticity), [tridentate](https://en.wikipedia.org/wiki/Tridentate_ligand), [tetradentate](https://en.wikipedia.org/wiki/Tetradentate_ligand), and [hexadentate](https://en.wikipedia.org/wiki/Hexadentate_ligand) ligands as well as conjugated [haptic ligands](https://en.wikipedia.org/wiki/Hapticity). +:::{tip} +Ligands and functional groups can be added not only to centers created with the Template Tool but to any atom that bears hydrogen atoms. -![Dialog of ligand types in Avogadro](../../_static/Template-LigandDialog.png) +For example, the Template Tool could be used to rapidly add acyl groups to sugar rings. +::: -After you change the type of ligand, the list of ligands will change accordingly. Similarly, after chosing a particular ligand, the preview image will update. +:::{tip} +The Template Tool is designed for quickly appending ligands and functional groups to an existing molecule. +Discrete small organic molecules can not be created with the Template Tool by clicking on an empty space. -For monodentate or haptic ligands, click on a hydrogen atom to attach the new ligand. +To create organic molecules with a single click, use [`Build`⇒`Insert`⇒`Molecule…`](menus-build-menu-insert) instead. +::: -![Example of ammine ligand attached to an octahedral iron atom](../../_static/Template-Ligand.png) +## Pane options -For bidentate, tridentate, tetradentate, and hexadentate ligands, click on multiple hydrogen atoms and the ligand will be attached accordingly. For example for a tridentate ligand, click on three atoms in order. If you click on three sites in a line, but the tridentate ligand is a triangle, Avogadro will attach a "best fit." +Switching tabs chooses between the creation of centers, ligands, and functional groups, and presents different options in the pane. -![Iron bipyridine molecule](../../_static/FeBipy.png) +### Centers tab -## Attaching Functional Groups +Element +: Select the element of new centers. -Functional groups are similar to monodentate ligands in that they attach to a molecule through one new bond. + The currently selected element can be changed by selecting from the `Element` drop-down menu. + Various common elements are shown for easy access, but any element can be selected from the periodic table by choosing **Other…**. -Beyond the common choices, "Other…" includes a library of over 100 functional groups organized by element, e.g., sulfonates, acid anhydrides, boronic acids, etc. + ![Menu of elements, including carbon, phosphorus, sulfur, and transition metals](../../_static/Template-Element.png){height=300px align=center} -![Selecting other functional groups in a dialog organized by element](../../_static/OtherFunctionalGroup.png) +Formal Charge +: Set the formal charge assigned to new centers. -After selecting a group, a preview will appear. Click the "Insert" button and click on a hydrogen atom in the scene to attach the fragment of your choice. + Ions can be created by setting their charge via the drop-down. + Atoms' formal charges are not shown visually but are used to calculate the total molecular charge for a calculation or force field optimization. + Formal charges can be viewed and edited in [Atom Properties](panes-properties-atom). -## Creating New Ligands +Coordination +: Select the coordination geometry of new centers. + + The `Coordination` drop-down allows the specification of the valency and geometry of the atom, including common arrangements of one to eight ligands. + This includes linear, trigonal planar, tetrahedral, square planar, trigonal bipyramidal, octahedral, as well as less common geometries such as square pyramidal, trigonal prism, pentagonal bipyramidal, and square antiprism. + + A preview of the selected coordination geometry is shown below the drop-down. + + ![Menu of coordination geometries including linear, trigonal planar, tetrahedral, square planar, trigonal bipyramidal, and octahedral](../../_static/Template-Coordination.png){height=300px align=center} + +### Ligands tab + +Type +: Specify the denticity or hapticity of the ligand. + + The drop-down allows selection from a range of ligand denticities, including common [bidentate](https://en.wikipedia.org/wiki/Denticity), [tridentate](https://en.wikipedia.org/wiki/Tridentate_ligand), [tetradentate](https://en.wikipedia.org/wiki/Tetradentate_ligand), and [hexadentate](https://en.wikipedia.org/wiki/Hexadentate_ligand) ligands, as well as conjugated [haptic ligands](https://en.wikipedia.org/wiki/Hapticity). + + By choosing **From Clipboard**, a ligand that has been copied to the clipboard can be used. + For further details on creating ligands, see below. + +Ligand +: Choose a specific ligand to be created. + + The drop-down is used to choose a specific ligand. + Its contents will update based on the choice of `Type`. + Various common ligands are shown for easy access, but more can be selected from the library by choosing **Other…**. + + A preview of the selected ligand and its attachment point is shown below the drop-down. + + For monodentate or haptic ligands, left-click on a hydrogen atom to attach the new ligand. + + ![Example of ammine ligand attached to an octahedral iron atom](../../_static/Template-Ligand.png){height=300px align=center} + + For bidentate, tridentate, tetradentate, and hexadentate ligands, one hydrogen atom must be left-clicked for each attachment point. + For example, for a tridentate ligand, click on three atoms in order. + If the shape of the sites chosen does not match the ligand template (e.g. three sites in a line are chosen, but the tridentate ligand is a triangle), Avogadro will attempt a "best fit". + + ![Iron bipyridine molecule](../../_static/FeBipy.png){height=300px align=center} + +### Groups tab + +Functional groups are similar to monodentate ligands in that they attach to a molecule through one new bond, and there is some overlap in the available fragments. + +However, the focus is on covalently bonded organic moieties. + +Group +: Choose a functional group to be created. + + The currently selected functional group can be changed by selecting from the drop-down menu. + Various common groups are shown for easy access, but more can be selected from the library by choosing **Other…**. + The library contains over 100 functional groups organized by element including sulfonates, acid anhydrides, boronic acids, and many more. + + ![Selecting other functional groups in a dialog organized by element](../../_static/OtherFunctionalGroup.png){height=300px align=center} + + A preview of the selected functional group and its attachment point is shown below the drop-down. + +## Creating new ligands While the ligand library includes many common ligands, you may wish to create your own or tweak a ligand before attachment. -As an example, we will build the salen ligand and add the attachment point for this tetradentate ligand. The process is similar for other ligands -- Avogadro will use the location of a dummy atom (element zero) to determine where to attach to a metal or molecule. +An existing structure open in Avogadro can be easily turned into a ligand. +It could have been, for example, drawn by hand, or loaded from a calculation output file. + +To demonstrate, we will build the salen ligand and add the attachment point for this tetradentate ligand using a dummy atom (an atom of element 0). +The process is similar for other ligands -- Avogadro will use the location of a dummy atom to determine where to attach to a metal or molecule. -After creating your ligand molecule, you should select the atoms which will be the attachement sites: +After creating your ligand molecule, select the atoms which will be the attachment sites: -![salen molecule with four selected atoms: two oxygen and two nitrogen](../../_static/Ligand-SelectAtoms.png) +![salen molecule with four selected atoms: two oxygen and two nitrogen](../../_static/Ligand-SelectAtoms.png){height=300px align=center} -The Build ⇒ Add Centroid command will add a dummy atom at the center of the selected atoms: +The `Build`⇒`Add Centroid` command will add a dummy atom at the center of the selected atoms: -![menu indicating "Add Centroid" command](../../_static/Ligand-CentroidMenu.png) +![menu indicating "Add Centroid" command](../../_static/Ligand-CentroidMenu.png){height=300px align=center} -The ligand will now have a centroid dummy atom added. Draw bonds as desired to the attachment sites. +The ligand will now have a centroid dummy atom added. +The dummy atom can be manipulated in the same way as any other atom. +Draw bonds as desired between the dummy atom and the attachment sites. -![salen ligand with four selected atoms and new centroid dummy atom](../../_static/Ligand-AddCentroid.png) +![salen ligand with four selected atoms and new centroid dummy atom](../../_static/Ligand-AddCentroid.png){height=300px align=center} -The ligand can either be copied to the clipboard to insert via the Clipboard ligand type, or saved as CJSON to contribute to the [fragment repository](https://github.com/openchemistry/fragments) +The ligand can either be copied to the clipboard to allow insertion via the **From Clipboard** ligand type, or saved as CJSON to contribute to the [fragment repository](https://github.com/openchemistry/fragments). -## Creating New Haptic Ligands +## Creating new haptic ligands Haptic ligands indicate bonding between a metal center and a delocalized pi system, such as an aromatic ligand. -As an example, we will build up an η4-cyclooctatetraene ligand. Either draw the molecule or use File ⇒ Import ⇒ Download by Name… to insert the basic molecule. +As an example, we will build up an η{sup}`4`-cyclooctatetraene ligand. +Either draw the molecule or use `File`⇒`Import`⇒`Download by Name…` to insert the basic molecule. -![cyclooctatetraene molecule](../../_static/Template-COD.png) +![cyclooctatetraene molecule](../../_static/Template-COD.png){height=300px align=center} Now select the four atoms to use for the haptic ligand: -![cyclooctatetraene molecule indicating four selected carbon atoms](../../_static/Template-COD2.png) +![cyclooctatetraene molecule indicating four selected carbon atoms](../../_static/Template-COD2.png){height=300px align=center} -Now use the "Add Centroid" command to add a dummy atom at the centroid of the selected atoms. This is useful to create distinct hapticity (e.g., η3 cyclopentadienyl after selecting three carbon atoms instead of five): +Now use the `Build`⇒`Add Centroid` command to add a dummy atom at the centroid of the selected atoms. +This is useful to create distinct hapticity (e.g. η{sup}`3`-cyclopentadienyl after selecting three carbon atoms instead of five): -![cyclooctatetraene molecule indicating four selected carbon atoms and dummy attachment point](../../_static/Template-COD3.png) +![cyclooctatetraene molecule indicating four selected carbon atoms and dummy attachment point](../../_static/Template-COD3.png){height=300px align=center} -For a haptic ligand, we need one more dummy atom, perpendicular to the pi system. We can add an additional dummy atom **perpendicular** to the centroid: +For a haptic ligand, we need one more dummy atom, perpendicular to the pi system. +We can add an additional dummy atom **perpendicular** to the centroid using the `Build`⇒`Add Perpendicular` command: -![Menu indicating "Add Perpendicular" item for haptic attachment points](../../_static/Template-LigandPerpendicular.png) +![Menu indicating "Add Perpendicular" item for haptic attachment points](../../_static/Template-LigandPerpendicular.png){height=300px align=center} After adding the perpendicular attachment, draw a bond between the centroid and the attachment site. -![](../../_static/Template-COD4.png) +![](../../_static/Template-COD4.png){height=300px align=center} -You can either save this file as CJSON to contribute to the repository, or "Select None" to deselect all atoms and copy the ligand to insert into a new molecule. +As before, you can either save this file as CJSON to contribute to the repository, or copy the ligand to the clipboard to insert into a new molecule. diff --git a/_sources/docs/tutorials/drawing-simple-molecules.md.txt b/_sources/docs/tutorials/drawing-simple-molecules.md.txt new file mode 100644 index 00000000..77eeefbe --- /dev/null +++ b/_sources/docs/tutorials/drawing-simple-molecules.md.txt @@ -0,0 +1,55 @@ +(tutorials-drawing-simple-molecules)= + +# Drawing Simple Molecules + +## First steps + +Left-clicking on the display will allow you to begin your journey into molecule creation. A left-click will create a carbon atom. A right-click will delete the atom. + +![](../../_static/first-carbon.png) + +Left-clicking the initial atom and dragging your mouse will create a bond to another carbon atom. + +![](../../_static/drag-to-build.png) + +Avogadro uses carbon as the default element. A different element can be selected through the `Element` drop-down menu. +Typing the atomic symbol (e.g., O for Oxygen, As for Arsenic) is a shortcut for changing the selected element. + +![](../../_static/pick-an-element.png) + +## Water + +Let's say you wanted to create water. You can either type in "O", or select "Oxygen (8)" from the drop-down menu, and then click on the black display. + +Left-clicking on an atom that has already been generated will also change the element. +In this case, clicking on the initial carbon atom changed it into an oxygen atom. + +![](../../_static/tutorial-water.png) + +If the `Adjust Hydrogens` box is checked, hydrogen atoms in the molecule will be automatically adjusted to satisfy valency (as shown above). + +![](../../_static/tutorial-adjust-hydrogens.png) + +Bond order is changed through the `Bond Order` drop-down menu, or by typing the numbers 1, 2, or 3. +Bonds are added by left-clicking on a bond that has already been created. Right-clicking on a bond deletes the bond. + +![](../../_static/tutorial-bond-order.png) + +```{tip} **New in 2.0** +The default bond order is "Automatic," and will adjust with the length of the bond. +``` + +## Carbon Dioxide + +Begin drawing the "O-C-O" structure. +After the skeleton is drawn, all you need to do is left-click on the bonds to make them into double bonds. +Left-clicking on the bonds will create a double bond (shown below). + +![](../../_static/tutorial-co2-step1.png) +![](../../_static/tutorial-co2-step2.png) +![](../../_static/tutorial-co2-step3.png) + +Once you've created your molecule, you can optimize its geometry through the `Extensions` menu. +Selecting the `Extensions` menu, and clicking `Optimize Geometry` will provide your molecule with proper bond lengths and angles. + +![](../../_static/ada26872-ede7-4601-bd4e-d790c10ad614.png) \ No newline at end of file diff --git a/_sources/docs/tutorials/index.md.txt b/_sources/docs/tutorials/index.md.txt index 04f49a24..5c787e5d 100644 --- a/_sources/docs/tutorials/index.md.txt +++ b/_sources/docs/tutorials/index.md.txt @@ -7,6 +7,7 @@ caption: Tutorials --- +drawing-simple-molecules naming-a-molecule viewing-molecular-orbitals viewing-vibrations diff --git a/_sources/docs/whats-new-in-avogadro-2/interface-changes.md.txt b/_sources/docs/whats-new-in-avogadro-2/interface-changes.md.txt index e9d4e6f7..b2e12032 100644 --- a/_sources/docs/whats-new-in-avogadro-2/interface-changes.md.txt +++ b/_sources/docs/whats-new-in-avogadro-2/interface-changes.md.txt @@ -12,17 +12,17 @@ Consequently, this documentation is still a work in progress. Some instructions ## Save vs Export ```{warning} -`File` ⇒ `Save` now only allows saving to CJSON and CML formats. +`File`⇒`Save` now only allows saving to CJSON and CML formats. -All other formats are now **exported** instead, using `File` ⇒ `Export` ⇒ `Molecule…` +All other formats are now **exported** instead, using `File`⇒`Export`⇒`Molecule…` ``` -In Avogadro 1.0–1.2, users would be surprised that when saving to some formats (e.g., XYZ, PDB) and bond orders or other information would be lost. As a result, `File` ⇒ `Save` is now reserved for saving to CJSON and CML formats, which will retain all data and options. +In Avogadro 1.0–1.2, users would be surprised that when saving to some formats (e.g., XYZ, PDB) and bond orders or other information would be lost. As a result, `File`⇒`Save` is now reserved for saving to CJSON and CML formats, which will retain all data and options. If you wish to **export** to other formats (e.g., XYZ, PDB, SDF, etc.) use -`File` ⇒ `Export` ⇒ `Molecule…` instead. +`File`⇒`Export`⇒`Molecule…` instead. -![Screenshot indicating File ⇒ Export ⇒ Molecule menu item](../../_static/FileExportMolecule.png) +![Screenshot indicating File⇒Export⇒Molecule menu item](../../_static/FileExportMolecule.png) ## Menu organization diff --git a/_sources/docs/whats-new-in-avogadro-2/major-new-features.md.txt b/_sources/docs/whats-new-in-avogadro-2/major-new-features.md.txt index d51f709e..9d94beea 100644 --- a/_sources/docs/whats-new-in-avogadro-2/major-new-features.md.txt +++ b/_sources/docs/whats-new-in-avogadro-2/major-new-features.md.txt @@ -50,7 +50,7 @@ Future development will enable the use layers for complex simulations (e.g., QM/ ### Symmetry properties -Avogadro 2 includes a new tool to perceive molecular symmetry, display symmetry elements, and explore subgroups and classes of symmetric atoms. You can find it under Analysis ⇒ Properties. +Avogadro 2 includes a new tool to perceive molecular symmetry, display symmetry elements, and explore subgroups and classes of symmetric atoms. You can find it under `Analysis`⇒`Properties`⇒`Symmetry…`.
Example of symmetry detection and rendering in C60

Example of symmetry detection and rendering on a C60 molecule, showing the inversion center and C5 rotations

diff --git a/_static/toolbar_dark.svg b/_static/toolbar_dark.svg new file mode 100644 index 00000000..34390223 --- /dev/null +++ b/_static/toolbar_dark.svg @@ -0,0 +1,1704 @@ + + + + diff --git a/_static/toolbar_light.svg b/_static/toolbar_light.svg new file mode 100644 index 00000000..08913e7b --- /dev/null +++ b/_static/toolbar_light.svg @@ -0,0 +1,1951 @@ + + + + diff --git a/docs/getting-started/drawing-molecules.html b/docs/getting-started/drawing-molecules.html index ba9c3780..9e60cd25 100644 --- a/docs/getting-started/drawing-molecules.html +++ b/docs/getting-started/drawing-molecules.html @@ -509,17 +509,17 @@

Drawing Molecules

Tip

New in 2.0 -You can also use the new Template Tool which makes it easier +You can also use the new Template Tool which makes it easier to attach functional groups or assemble inorganic and organometallic complexes.

Screenshot of the draw tool

-

With the Draw Tool selected, left-clicking on the view frame will begin your journey into molecule creation. A left-click will create a carbon atom. A right-click on the atom will delete it.

+

With the Draw Tool selected, left-clicking on the view pane will begin your journey into molecule creation. A left-click will create a carbon atom. A right-click on the atom will delete it.

Left-clicking the initial atom and dragging your mouse will create a second carbon atom with a bond from the initial atom.

Avogadro uses carbon as the default element. A different element can be selected through the Element drop-down menu in the Draw Pane. While the Draw Tool is active, typing an atomic symbol (e.g. O for oxygen, or As for arsenic) is a shortcut for changing the selected element.

-

Let’s say you wanted to create water. You can either type in O, or select “Oxygen (8)” from the drop-down menu, and then click on the black view.

+

Let’s say you wanted to create water. You can either type in O, or select “Oxygen (8)” from the drop-down menu, and then click on the (by default black) view pane.

Left-clicking on an atom that has already been generated will also change the element. In this case, clicking on the initial carbon atom changed it into an oxygen atom.

If the Adjust Hydrogens box in the Draw Pane is checked, hydrogen atoms in the molecule will be automatically added and removed to satisfy valency (as shown above).

diff --git a/docs/getting-started/making-selections.html b/docs/getting-started/making-selections.html index 5303ea52..aa0ee365 100644 --- a/docs/getting-started/making-selections.html +++ b/docs/getting-started/making-selections.html @@ -508,7 +508,7 @@

Making SelectionsSelection Tool is also a useful feature to master when beginning to learn Avogadro. Generally, the Selection Tool allows for the individual selection of atoms, bonds, or fragments.

The Selection Tool provides you with the ability to select a single atom within a molecule. This is achieved by left-clicking the atom. Pressing and holding shift while clicking allows for the selection of multiple atoms.

-

Right-clicking on an empty part of the view will clear the selection made.

+

Right-clicking on an empty part of the view pane will clear the selection made.

Warning

A known bug means that on some systems, multiple left-clicks are required to clear the selection.

diff --git a/docs/getting-started/saving-files.html b/docs/getting-started/saving-files.html index ea8c3f47..1a720049 100644 --- a/docs/getting-started/saving-files.html +++ b/docs/getting-started/saving-files.html @@ -512,7 +512,7 @@

Saving Files

Exporting to other formats#

If you wish to export to other formats (e.g., XYZ, PDB, SDF, etc.) use -File ⇒ Export ⇒ Molecule…

+File⇒Export⇒Molecule…

Screenshot indicating File => Export => Molecule menu item

Avogadro uses support for Open Babel to write to over 100 different chemical file formats.

diff --git a/docs/index.html b/docs/index.html index eb4a933c..c88745f4 100644 --- a/docs/index.html +++ b/docs/index.html @@ -499,12 +499,12 @@

Avogadro is designed for cross-platform use and is fully supported on Windows, Linux, and macOS.

Avogadro 2#

-

In particular, this manual covers the new release of Avogadro 2, a major update, and includes major changes, the revised interface, and new features. +

In particular, this manual covers the new release of Avogadro 2, a major update, and includes major changes, a revised interface, and new features. Most sections include notes on changes from v1.0, 1.1, and 1.2 to the new 2.0 release, though as there have been so many, coverage is not in any way comprehensive.

Versions 1.90 to 1.99 were beta releases of Avogadro 2 and a lot of this manual applied to those versions too, but note that during the beta phase there were also many improvements made to the UI which have changed the location or appearance of various things.

Look out for boxes highlighting new features or changes for Avogadro 2:

-

Added in version 2.0.

+

Added in version 2.0: This feature is new.

Changed in version 2.0: This feature now behaves differently.

diff --git a/docs/menus/build-menu.html b/docs/menus/build-menu.html index 06b27c09..31dc3a86 100644 --- a/docs/menus/build-menu.html +++ b/docs/menus/build-menu.html @@ -552,7 +552,7 @@

Remove Hydrogens

Insert#

-

“Insert” provides a faster, simpler way of building molecules. A depicted below, you can insert DNA/RNA, a Fragment, a Peptide, and can also insert a molecule based on SMILES text.

+

diff --git a/docs/panes/index.html b/docs/panes/index.html index b6eea4df..b0ba2194 100644 --- a/docs/panes/index.html +++ b/docs/panes/index.html @@ -468,7 +468,7 @@
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diff --git a/docs/panes/properties.html b/docs/panes/properties.html new file mode 100644 index 00000000..528c278d --- /dev/null +++ b/docs/panes/properties.html @@ -0,0 +1,576 @@ + + + + + + + + + + + <no title> — Avogadro 1.99.0 documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + \ No newline at end of file diff --git a/docs/panes/view-configuration.html b/docs/panes/view.html similarity index 99% rename from docs/panes/view-configuration.html rename to docs/panes/view.html index 9919ce9d..0ac098ec 100644 --- a/docs/panes/view-configuration.html +++ b/docs/panes/view.html @@ -44,8 +44,8 @@ - - + + @@ -505,7 +505,7 @@
- + diff --git a/docs/settings/language.html b/docs/settings/language.html index 98ad2081..7990d549 100644 --- a/docs/settings/language.html +++ b/docs/settings/language.html @@ -470,7 +470,7 @@

Language#

-

By default Avogadro will use your system language, but you can change this by going to Extensions ⇒ User Interface Language….

+

By default Avogadro will use your system language, but you can change this by going to Extensions⇒User Interface Language….

Avogadro is available in many languages. Languages with significant coverage as of v1.99 include English (US, GB, AU, CA), Chinese, Esperanto, French, Georgian, German, Hungarian, Japanese, Korean, Portuguese (PT, BR), Serbian, Spanish, and Turkish. Many others have partial coverage and are in progress all the time!

Translation is an ongoing community effort so there are likely to be many errors or inconsistencies. If you find something wrong or missing, please suggest improvements!

If you would like to fix a mistranslation, add support for a language you speak, or contribute to a partially translated one, we’d love it – see here for information on contributing.

diff --git a/docs/tools/align-tool.html b/docs/tools/align-tool.html index 5afdbe7a..2adc13be 100644 --- a/docs/tools/align-tool.html +++ b/docs/tools/align-tool.html @@ -433,6 +433,7 @@
  • Navigation Tool
  • Draw Tool
  • Template Tool
    • +
  • Label Tool
  • Selection Tool
  • Manipulation Tool
  • Bond-Centric Manipulation Tool
    • @@ -514,8 +515,10 @@

    The Align Tool is used to rotate and translate a molecule(s) so that it aligns with one of the Cartesian axes.

    Basic usage#

    -

    First, an alignment axis is chosen from the Axis drop-down menu in the Align Pane. The x, y, and z keys on the keyboard are shortcuts for changing the alignment axis.

    -

    Secondly, select either one or two atoms in the view frame with the left mouse button. The labels #1 and #2 will be displayed on each.

    +

    First, an alignment axis is chosen from the Axis drop-down menu in the Align Pane. +The x, y, and z keys on the keyboard are shortcuts for changing the alignment axis.

    +

    Secondly, select either one or two atoms in the view frame with the left mouse button. +The labels #1 and #2 will be displayed on each.

    Clicking Align will then reposition the molecule as desired.

    If only one atom was selected, the molecule will simply be translated so that it is placed at the origin (i.e. the Cartesian coordinates (0,0,0)).

    If two atoms were selected, the first will be placed at the origin, and the second will be placed along the chosen axis.

    @@ -529,7 +532,8 @@

    Pane options

    The Axis drop-down menu allows you to choose which Cartesian axis the molecule will be aligned to.

    -

    By default, the relative positions of everything in the view frame will remain the same and the same transformation will be applied to all objects. By choosing the “Molecule” option in the Align drop-down menu in the Align Pane, only the molecule containing the selected atoms will be affected by the change.

    +

    By default, the relative positions of everything in the view frame will remain the same and the same transformation will be applied to all objects. +By choosing the “Molecule” option in the Align drop-down menu in the Align Pane, only the molecule containing the selected atoms will be affected by the change.

    diff --git a/docs/tools/animation-tool.html b/docs/tools/animation-tool.html index b9cb0433..baeb0315 100644 --- a/docs/tools/animation-tool.html +++ b/docs/tools/animation-tool.html @@ -433,6 +433,7 @@
  • Navigation Tool
  • Draw Tool
  • Template Tool
    • +
  • Label Tool
  • Selection Tool
  • Manipulation Tool
  • Bond-Centric Manipulation Tool
    • @@ -511,6 +512,7 @@

    Animation Tool#

    The icon of the Animation Tool in light mode.

    +

    Keyboard shortcut: Ctrl+9

    diff --git a/docs/tools/auto-rotate-tool.html b/docs/tools/auto-rotate-tool.html index 47f16e6b..1ce4fb1f 100644 --- a/docs/tools/auto-rotate-tool.html +++ b/docs/tools/auto-rotate-tool.html @@ -472,7 +472,8 @@

    Auto-Rotate Tool#

    The auto rotate tool allows for the continuous rotation of a molecule.

    -

    To rotate the molecule, adjust the x, y, and z rotation scales as desired. Then select “Start”.

    +

    To rotate the molecule, adjust the x, y, and z rotation scales as desired. +Then select “Start”.

    You can also click and drag from an atom to rotate the molecule in a specific direction.

    diff --git a/docs/tools/bond-centric-manipulation-tool.html b/docs/tools/bond-centric-manipulation-tool.html index 20606af6..729d8380 100644 --- a/docs/tools/bond-centric-manipulation-tool.html +++ b/docs/tools/bond-centric-manipulation-tool.html @@ -433,6 +433,7 @@
  • Navigation Tool
  • Draw Tool
  • Template Tool
    • +
  • Label Tool
  • Selection Tool
  • Manipulation Tool
  • Bond-Centric Manipulation Tool
    • @@ -510,7 +511,14 @@

    Bond-Centric Manipulation Tool#

    +

    The icon of the Bond-Centric Manipulation Tool in light mode.

    +

    Keyboard shortcut: Ctrl+7

    The Bond-Centric Manipulation Tool is a powerful tool that allows you to focus on a specific bond and change its length and the surrounding angles, while keeping the rest of the molecule the same.

    +
    +

    Tip

    +

    The Bond-Centric Manipulation Tool provides mouse-based manual adjustment of bond lengths and angles. +If you wish to set these quantities to specific, exact values, it may be more convenient to do this in the relevant Properties pane.

    +

    Starting with the basics:#

    diff --git a/docs/tools/draw-tool.html b/docs/tools/draw-tool.html index e1931fe0..8daa6239 100644 --- a/docs/tools/draw-tool.html +++ b/docs/tools/draw-tool.html @@ -433,6 +433,7 @@
  • Navigation Tool
  • Draw Tool
  • Template Tool
    • +
  • Label Tool
  • Selection Tool
  • Manipulation Tool
  • Bond-Centric Manipulation Tool
    • @@ -510,39 +511,78 @@

    Draw Tool#

    -

    Molecules are built and edited with the Draw Tool, which allows “free-hand” sketching of new molecules.

    +

    The icon of the Draw Tool in light mode.

    +

    Keyboard shortcut: Ctrl+2

    +

    Molecules are built and edited with the Draw Tool, which allows “free-hand” sketching of new molecules.

    Tip

    -

    New in 2.0 -You can also use the new Template Tool, which makes it quicker and easier to attach functional groups or assemble inorganic/organometallic complexes.

    +

    To help rapidly build your structure you can also use the new Template Tool, which makes it quicker and easier to attach functional groups or assemble inorganic/organometallic complexes.

    -

    Screenshot of the draw tool

    -

    Left-clicking on the display will allow you to begin your journey into molecule creation. A left-click will create a carbon atom. A right-click will delete the atom.

    -

    -

    Left-clicking the initial atom and dragging your mouse will create a bond to another carbon atom.

    -

    -

    Avogadro uses carbon as the default element. A different element can be selected through the Element drop-down menu. Typing the atomic symbol (e.g., O for Oxygen, As for Arsenic) is a shortcut for changing the selected element.

    -

    -

    Let’s say you wanted to create water. You can either type in “O”, or select “Oxygen (8)” from the drop-down menu, and then click on the black display.

    -

    Left-clicking on an atom that has already been generated will also change the element. In this case, clicking on the initial carbon atom changed it into an oxygen atom.

    -

    -

    If the Adjust Hydrogens box is checked, hydrogen atoms in the molecule will be automatically adjusted to satisfy valency (as shown above).

    -

    -

    Bond order is changed through the Bond Order drop-down menu, or by typing the numbers 1, 2, or 3. Bonds are added by left-clicking on a bond that has already been created. Right-clicking on a bond deletes the bond.

    -

    +
    +

    Added in version 2.0: The default bond order setting is now Automatic – it will adjust intelligently with the length of the bond.

    +
    +
    +

    Basic usage#

    +

    Atoms and bonds are drawn using the mouse.

    +

    Left-click on an empty space in the view pane to create an atom of the currently selected element.

    +

    Left-click on an existing atom to change its element to the one currently selected.

    +

    Left-click and drag from an atom to create a new bond starting from that atom. +A new atom of the currently selected element is automatically created at the end of the new bond and is visible while dragging.

    +
    +

    Tip

    +

    New atoms and bonds will be created in a plane that is parallel to the screen and includes the atom the bond originates from.

    +
    +

    If, during the drag, the mouse is moved over an existing atom, the mouse will “snap” to it, and the new atom will disappear. +The new bond will be drawn to this existing atom instead.

    +

    By default, the bond order of a new bond is selected automatically based on the distance between the atoms: long bonds will be single bonds, short bonds will be double bonds, and very short bonds will be triple bonds.

    +

    Left-click on an existing bond to increase its bond order by one. +Left-clicking on a triple bond turns it back into a single bond.

    +

    Delete atoms and bonds by right-clicking on them.

    +
    +
    +

    Pane options#

    +
    +
    Element

    Choose the element of new atoms.

    +

    Various common elements are shown in the drop-down for easy access, but any element can be selected from the periodic table by choosing Other…. +Used elements are remembered and will appear in the drop-down in future.

    +

    Alternatively, use the handy keyboard shortcuts – just type the atomic symbol of the desired element (e.g., O for Oxygen, As for Arsenic).

    +
    +
    Bond Order

    Choose the bond order of new bonds.

    +

    There are keyboard shortcuts for this too – 1 selects single, 2 double, and so on.

    +

    When the bond order setting is set to Automatic (default), new bonds are given a bond order based on their length. +The cut-offs are determined by the elements of the atoms at either end of the bond.

    Tip

    -

    New in 2.0 -The default bond order is “Automatic,” and will adjust with the length of the bond.

    +

    Single bonds are created when the bond length exceeds the sum of the atoms’ covalent radii. +Double bonds are created when the bond length is between 91% and 100% of the sum of the covalent radii, and anything shorter than 91% becomes a triple bond.

    +

    For a carbon-carbon bond, the lower cut-offs are thus approx. 1.52 Å for a single bond and 1.38 Å for a double.

    +
    +
    +
    Adjust Hydrogens

    Toggle automatically addition and removal of hydrogen atoms to fill valencies.

    +

    If this box is checked (default), extra hydrogen atoms will be automatically added to new atoms to satisfy their valency. +When a bond is created or the order of a bond is changed, the number of hydrogen atoms on the atoms at each end of the bond will also be adjusted.

    +

    For main-group elements, the default valency is always that predicted by the octet rule, while metal atoms are always created alone, without bonded atoms. +To create metal centers or hypervalent main-group centers, it is often better to use the Template Tool.

    +
    +

    Warning

    +

    It may not be possible to deliberately add or remove hydrogen atoms (for example, to create a radical or an ion) while this setting is checked.

    +

    If this is desired, turn off the setting while manually adjusting the hydrogens. +Turning the setting back on will not cause the number of hydrogen atoms to be readjusted.

    -
    -

    Creating Carbon Dioxide#

    -

    Begin drawing the “O-C-O” structure. After the structure is drawn, all you need to do is left-click on the bonds. Left-clicking on the bonds will create a double bond (shown below).

    -

    - -

    -

    Once you’ve created your molecule, you can optimize its geometry through the Extensions menu. Selecting the Extensions menu, and clicking Optimize Geometry will provide your molecule with proper bond lengths and angles.

    -

    +
    +
    +
    +
    +

    Adjusting the structure#

    +

    It is challenging to draw structures in 3D on a 2D screen. +Using the Draw Tool alone will probably not give you a molecule that looks sensible and is representative of the real geometry.

    +

    For manual adjustment, the position of the atoms can be fine-tuned by using the Manipulation Tool in combination with the Navigation Tool to rotate and pan the view.

    +

    To quickly get a sensible geometry, make use of the Optimize Geometry extension. +This can be conveniently activated using the shortcut Ctrl+Alt+O.

    +
    +
    +

    Tutorial#

    +

    A step-by-step tutorial for some simple molecules can be found here.

    @@ -592,7 +632,10 @@

    Creating Carbon Dioxide

    diff --git a/docs/tools/index.html b/docs/tools/index.html index 4bcc0f8d..49277025 100644 --- a/docs/tools/index.html +++ b/docs/tools/index.html @@ -433,6 +433,7 @@
  • Navigation Tool
  • Draw Tool
  • Template Tool
    • +
  • Label Tool
  • Selection Tool
  • Manipulation Tool
  • Bond-Centric Manipulation Tool
    • @@ -508,15 +509,20 @@

    Tools#

    Each tool in Avogadro has an associated icon in the toolbar:

    -

    Toolbar

    -

    Hovering over a tool with the mouse gives a brief description of how to use it.

    -

    After selecting a tool, the name of the tool and any options available for the tool are displayed in the Tool Pane.

    +

    The appearance of the toolbar in dark mode.

    +

    Within Avogadro, hovering over a tool icon with the mouse gives a brief description of how to use it.

    +

    Tools can be selected either by left-clicking the icon, or using the keyboard by pressing Ctrl and the corresponding number key (1 through 9 and 0, left to right).

    +

    After selecting a tool, the name of the tool and any options available for the tool are displayed to the left in the Tool pane.

    +
    +

    Added in version 2.0: The Template Tool, Label Tool and Animation Tool are all completely new tools.

    +

    Tools

    • Navigation Tool
    • Draw Tool
    • Template Tool
      • +
    • Label Tool
    • Selection Tool
    • Manipulation Tool
    • Bond-Centric Manipulation Tool
      • diff --git a/docs/tools/label-tool.html b/docs/tools/label-tool.html new file mode 100644 index 00000000..4238e184 --- /dev/null +++ b/docs/tools/label-tool.html @@ -0,0 +1,663 @@ + + + + + + + + + + + Label Tool — Avogadro 1.99.0 documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      + + + + + + + + + + +
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      +
      +
      + + + Ctrl+K +
      +
      + +
      + +
      + + +
      +
      + + + +
      + +
      + + + + + +
      + +
      + +
      + +
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      + + + + + +
      + +
      +

      Label Tool#

      +

      The icon of the Label Tool in light mode.

      +

      Keyboard shortcut: Ctrl+3

      +

      The Label Tool is used to add custom text to atoms.

      +
      +

      Basic usage#

      +

      Left-click on an atom to create a new label. +A cursor will appear.

      +

      Type the desired label with the keyboard.

      +

      Press Enter or click anywhere else in the view pane to confirm the new label.

      +
      +

      Warning

      +

      By default, atom labels are not visible in Avogadro!

      +

      To show labels, enable the Labels display type in the Display Types pane. Open the options for the Labels display type by clicking the three bullets ⋯

      +

      Then, to show the custom labels, in the Atom Label drop-down of the Display Type Configuration pane, change the selected label type to Custom.

      +
      +

      Edit an existing label by left-clicking on it. +Its position will raise slightly to indicate that it is being edited.

      +
      +
      +

      Pane options#

      +

      There are currently no options for this tool in the Edit Labels pane.

      +

      The Label Tool is a work in progress and the ability to customize individual labels will likely come in future releases.

      +

      Display settings for all labels, such as text color and placement, can be changed in the Display Type Configuration pane for the Labels display type.

      +
      +
      + + +
      + + + + + + + +
      + + + +
      + + +
      +
      + On this page +
      +
      + +
      + + +
      + + + + + + Edit on GitHub + + + +
      +
      + +
      + + +
      +
      + +
      + +
      +
      +
      + + + + + + + + \ No newline at end of file diff --git a/docs/tools/manipulation-tool.html b/docs/tools/manipulation-tool.html index 0464a0c0..d3ec6d80 100644 --- a/docs/tools/manipulation-tool.html +++ b/docs/tools/manipulation-tool.html @@ -433,6 +433,7 @@
    • Navigation Tool
    • Draw Tool
    • Template Tool
      • +
    • Label Tool
    • Selection Tool
    • Manipulation Tool
    • Bond-Centric Manipulation Tool
      • @@ -510,33 +511,59 @@

      Manipulation Tool#

      -

      The Manipulation Tool allows you to move individual atoms as well as fragments.

      -

      -

      If one or more atoms have been selected with the Selection Tool, all operations will be carried out on the entire selection as one unit. If nothing has been selected, whichever atom is dragged will be moved.

      +

      The icon of the Manipulation Tool in light mode.

      +

      Keyboard shortcut: Ctrl+6

      +

      The Manipulation Tool allows you to move atoms, molecules, and fragments.

      Basic usage#

      -

      Atoms can be translated by clicking and dragging with the left mouse button.

      +

      Click and drag an atom to manipulate it.

      +

      The Manipulation Tool operates in two different modes:

      +
        +

      1. If one or more atoms have been selected, for example with the Selection Tool, all transformations will be carried out on the entire current selection as one unit.

        2. +

      2. If nothing has been selected, whichever atom is clicked will be moved.

        3. +
      +

      Translate atoms or fragments by clicking and dragging them with the left mouse button.

      Tip

      -

      When translating with click and drag, atoms will always move parallel to the screen; their depth will not change. For effective positioning within 3D space, it is thus necessary to combine the Manipulation Tool with the Navigation Tool to rotate the molecule.

      +

      When translating with click and drag, atoms will always move parallel to the screen; their depth will not change. +For effective positioning within 3D space, it is thus necessary to combine the Manipulation Tool with the Navigation Tool to rotate the molecule.

      -

      Atoms can be rotated by clicking and dragging with the right mouse button.

      +

      Rotate atoms or fragments by clicking and dragging them with the right mouse button. +On a single atom this will have no visible effect.

      Tip

      Rotation with click and drag will always be about the geometric center of the selection.

      -

      The Manipulation Tool is automatically selected after inserting a fragment, to enable quick and easy positioning of the new fragment.

      +

      The Manipulation Tool is automatically selected after inserting a fragment via Build⇒Insert, to enable quick and easy positioning of the new fragment.

      Pane options#

      The options in the Manipulate Pane allow you to apply transformations mathematically to the currently selected atoms.

      -

      Shifts along the X-, Y-, and Z-axes can be specified in angstrom.

      -

      -

      The “Rotate around:” section allows you to rotate your selection around the current geometry, or the origin. After choosing how many degrees to rotate your selection click “Apply”.

      -

      -

      Clicking “Reset” will reset all information in the translation, and rotation boxes. This does not reset the molecule, if you want to undo your adjustments go to the “Edit” menu in the top bar and select “Undo Manipulate Atom”.

      -

      +
      +
      Translate by:

      Specify the distances, in angstrom, to shift the selection along the X-, Y-, and Z-axes.

      +
      +
      +

      Applying a mathematical translation.

      +
      +
      Rotate around:

      Specify the angles, in degrees, to rotate the selection around the X-, Y-, and Z-axes, as well as the centre of the rotation.

      +

      The rotation can be carried out around the center of the current geometry or the origin, selected from the drop-down menu. +The X-, Y-, and Z-axes used for the rotation will be considered to intersect at this point.

      +
      +
      +

      Applying a mathematical rotation.

      +
      +
      Apply

      Apply the specified transformations to the current selection.

      +

      If values for both translation and rotation have been entered, both will be applied.

      +
      +
      Reset

      Reset all values in the translation and rotation boxes to 0.

      +

      This does not reset the molecule or reverse any transformations; if you want to undo your adjustments, go to the Edit menu in the top bar and select Undo Manipulate Atom.

      +
      +
      +

      Undoing transformations.

      +
      +

      Note

      The icon for the Manipulation Tool is adapted from a design by Ryan Dell, a contributor to the Noun Project.

      +
      diff --git a/docs/tools/measure-tool.html b/docs/tools/measure-tool.html index 0ef9f7f4..f11b1451 100644 --- a/docs/tools/measure-tool.html +++ b/docs/tools/measure-tool.html @@ -433,6 +433,7 @@
    • Navigation Tool
    • Draw Tool
    • Template Tool
      • +
    • Label Tool
    • Selection Tool
    • Manipulation Tool
    • Bond-Centric Manipulation Tool
      • @@ -510,13 +511,17 @@

      Measure Tool#

      +

      The icon of the Measure Tool in light mode.

      +

      Keyboard shortcut: Ctrl+8

      The measure tool determines bond lengths, angles, and dihedrals.

      The measure tool allows you to select and assess up to four atoms.

      -

      As you click on atoms Avogadro will automatically calculate the distances between atoms in a respective order. For example, the distance between atom 1 and 2 is 1.376 Å (displayed below).

      +

      As you click on atoms Avogadro will automatically calculate the distances between atoms in a respective order. +For example, the distance between atom 1 and 2 is 1.376 Å (displayed below).

      -

      Avogadro will also determine the angle between atoms, if at least three atoms have been selected. The second atom is used as the vertex.

      +

      Avogadro will also determine the angle between atoms, if at least three atoms have been selected. +The second atom is used as the vertex.

      If four atoms are selected, a dihedral angle is determined.

      diff --git a/docs/tools/navigation-tool.html b/docs/tools/navigation-tool.html index 13581db6..19f1c0c3 100644 --- a/docs/tools/navigation-tool.html +++ b/docs/tools/navigation-tool.html @@ -433,6 +433,7 @@
    • Navigation Tool
    • Draw Tool
    • Template Tool
      • +
    • Label Tool
    • Selection Tool
    • Manipulation Tool
    • Bond-Centric Manipulation Tool
      • @@ -509,19 +510,39 @@
      @@ -563,6 +584,19 @@

      Navigation Tool +
      + On this page +
      +

    + +
    diff --git a/docs/tools/selection-tool.html b/docs/tools/selection-tool.html index e5892848..f930efce 100644 --- a/docs/tools/selection-tool.html +++ b/docs/tools/selection-tool.html @@ -49,7 +49,7 @@ - + @@ -433,6 +433,7 @@
  • Navigation Tool
  • Draw Tool
  • Template Tool
    • +
  • Label Tool
  • Selection Tool
  • Manipulation Tool
  • Bond-Centric Manipulation Tool
    • @@ -510,16 +511,90 @@

    Selection Tool#

    -

    The selection tool allows the individual selection of atoms, bonds, or fragments.

    -

    -

    The select provides you with the ability to select a single atom within a molecule. This is achieved by left clicking the atom. Press and holding the “shift” key allows for the selection of multiple atoms.

    -

    Right clicking on the black display will clear the selection made.

    -

    -

    You can also double-click on an atom to select all atoms connected in that fragment or molecule.

    -

    -

    Clicking and dragging your cursor is another way molecules, or fragments of molecules can be selected.

    -

    -

    More information on selections can be found in the “Select” menu.

    +

    The icon of the Selection Tool in light mode.

    +

    Keyboard shortcut: Ctrl+5

    +

    The Selection Tool is used to select atoms with the mouse, either by individually picking them out or using a marquee selection box.

    +
    +

    Tip

    +

    Further useful selection functionality is available in the Select menu.

    +
    +
    +

    Basic usage#

    +

    Left-click on an individual atom to select it.

    +

    A single atom selected after clicking on it.

    +

    Left-click and drag to select multiple atoms by drawing a marquee selection box that covers the desired selection.

    +

    A selection box as visible while dragging.

    +

    Double-left-click on an atom to instantly select all connected atoms. +“Connected” atoms are any that can be traced to the clicked atom through bonds, including over multiple bonds i.e. the whole molecule.

    +

    An entire molecule selected after clicking on one of its constituent atoms.

    +
    +

    Tip

    +

    Use Select⇒Enlarge Selection to increase the selection from an atom to only its immediate neighbors rather than the whole molecule.

    +
    +

    Holding Shift or Ctrl while doing the above actions modifies their behaviour.

    +

    The effects of the modifier keys are best summarized in the table below:

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

    with no modifier

    with Shift

    with Ctrl

    general effect

    select

    add

    toggle/invert

    click

    Atom is selected.

    Atom is added to selection.

    Atom is toggled between selected and unselected.

    click and drag

    All atoms within box are selected.

    All atoms within box are added to selection.

    Unselected atoms within box are selected, but selected atoms are deselected.

    double-click

    Whole molecule is selected.

    Whole molecule is added to selection.

    Unselected atoms within the molecule are selected, but selected atoms are deselected.

    effect on other atoms

    Other atoms are deselected.

    All previously selected atoms remain selected.

    Other atoms remain as they were.

    +
    +

    Note that while Ctrl and double-left-click inverts the selection, this only affects connected atoms, whereas when Select⇒Invert Selection is used, the inversion applies to all atoms.

    +

    Select all atoms using the keyboard shortcut Ctrl+A.

    +

    Clear the selection by right-clicking in an empty part of the view pane or using the keyboard shortcut Ctrl+Shift+A.

    +
    +

    Tip

    +

    The keyboard shortcuts for select/deselect all are always available, not only when the Selection Tool is the currently selected tool.

    +
    +
    +

    Warning

    +

    A known bug means that right-clicking to clear the selection does not work on some systems. A triple-left-click on empty space or a left-click on any currently selected atom should do the trick instead.

    +
    +
    +
    +

    Pane options#

    +
    +
    Apply Color

    Pick a color and apply it to the currently selected atoms.

    +

    Clicking the colored rectangle will open a color picker. +After choosing a color, click OK to apply it.

    +
    +
    Change Layer

    Move the selected atoms to a different layer.

    +

    Putting parts of a molecule, or members of an ensemble, into different layers allows different visual settings to be applied to different elements within the same “Molecule” (what Avogadro calls a file).

    +

    See Layers for more information on how to use them.

    +
    +
    +
    @@ -533,12 +608,12 @@

    previous

    -

    Template Tool

    +

    Label Tool

     +
    + On this page +
    +
    + +
    diff --git a/docs/tools/template-tool.html b/docs/tools/template-tool.html index 78059167..4bbbf369 100644 --- a/docs/tools/template-tool.html +++ b/docs/tools/template-tool.html @@ -48,7 +48,7 @@ - + @@ -433,6 +433,7 @@
  • Navigation Tool
  • Draw Tool
  • Template Tool
    • +
  • Label Tool
  • Selection Tool
  • Manipulation Tool
  • Bond-Centric Manipulation Tool
    • @@ -509,63 +510,133 @@
    -

    Template Tool#

    -

    The template tool makes it easy to build up molecules from pre-defined ligands or functional groups, for example metal complexes or organometallic species.

    -

    Template tool window indicating menus for element, formal charge, and coordination geometry

    -
    -

    Inserting Atoms with Specific Geometry#

    -

    The “Element” menu includes many common transition metals as well as carbon, phosphorous and sulfur, as well as “Other…” which brings up a periodic table to select any element.

    -

    Menu of elements, including carbon, phosphorus, sulfur, and transition metals

    -

    The “Formal Charge” menu allows you to specify a formal charge on the atom, which is used to calculate the total molecular charge for a calculation or force field optimization.

    -

    The “Coordination” menu allows you to specify the number of attachment points and geometry of the atom, including common arrangements from one to eight ligands. This includes linear, trigonal planar, tetrahedral, square planar, trigonal bipyramidal, octahedral, as well as less common geometries such as square pyramidal, trigonal prism, pentagonal bipyramidal, and square antiprism.

    -

    Menu of coordination geometries including linear, trigonal planar, tetrahedral, square planar, trigonal bipyramidal, and octahedral

    -

    After selecting a coordination type from the menu, the preview will update to reflect the geometry.

    -

    Once you have selected the element, formal charge (if desired), and coordination, click in the scene to insert the atom.

    -

    Image of octahedral iron atom with six white hydrogen atoms

    +

    Template Tool#

    +

    The icon of the Template Tool in light mode.

    +

    Keyboard shortcut: Ctrl+3

    +

    With the Template Tool, a variety of pre-built fragments can be created.

    +

    The Template Tool makes it easy to build up metal complexes or organometallic species from pre-defined coordination centers and ligands.

    +

    The Template Tool also enables rapid addition of functional groups to an organic framework.

    +
    +

    Added in version 2.0.

    +
    +
    +

    Basic usage#

    +

    Ligands and functional groups must be added to an existing atom (a “center”), whether this be an atom within an organic framework or a metal center.

    +

    Elements in the third period and below can often exhibit multiple different coordination geometries, which are not easily created using the Draw Tool. +To achieve these, use the “Centers” templates.

    +

    A center of any element and with any common coordination geometry can be selected from the Center tab of the Template pane. +Left-click on an empty space in the view pane to create a center with attached hydrogens at each coordination site.

    +

    Image of octahedral iron atom with six white hydrogen atoms.

    +

    Once at least one center is present, ligands or functional groups can be added. +The desired ligand or group can be selected from the respective tabs of the Template pane. +Left-click any hydrogen atom in the view pane to replace it with the ligand or functional group, with the attachment point as shown in the preview image.

    +
    +

    Tip

    +

    Ligands and functional groups can be added not only to centers created with the Template Tool but to any atom that bears hydrogen atoms.

    +

    For example, the Template Tool could be used to rapidly add acyl groups to sugar rings.

    +
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    Tip

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    The Template Tool is designed for quickly appending ligands and functional groups to an existing molecule. +Discrete small organic molecules can not be created with the Template Tool by clicking on an empty space.

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    To create organic molecules with a single click, use Build⇒Insert⇒Molecule… instead.

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    Pane options#

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    Switching tabs chooses between the creation of centers, ligands, and functional groups, and presents different options in the pane.

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    Centers tab#

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    Element

    Select the element of new centers.

    +

    The currently selected element can be changed by selecting from the Element drop-down menu. +Various common elements are shown for easy access, but any element can be selected from the periodic table by choosing Other….

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    Menu of elements, including carbon, phosphorus, sulfur, and transition metals

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    Formal Charge

    Set the formal charge assigned to new centers.

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    Ions can be created by setting their charge via the drop-down. +Atoms’ formal charges are not shown visually but are used to calculate the total molecular charge for a calculation or force field optimization. +Formal charges can be viewed and edited in Atom Properties.

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    Coordination

    Select the coordination geometry of new centers.

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    The Coordination drop-down allows the specification of the valency and geometry of the atom, including common arrangements of one to eight ligands. +This includes linear, trigonal planar, tetrahedral, square planar, trigonal bipyramidal, octahedral, as well as less common geometries such as square pyramidal, trigonal prism, pentagonal bipyramidal, and square antiprism.

    +

    A preview of the selected coordination geometry is shown below the drop-down.

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    Menu of coordination geometries including linear, trigonal planar, tetrahedral, square planar, trigonal bipyramidal, and octahedral

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    Attaching Ligands#

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    The second tab in the template tool window allows you to select from a range of ligand types, including common bidentate, tridentate, tetradentate, and hexadentate ligands as well as conjugated haptic ligands.

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    Dialog of ligand types in Avogadro

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    After you change the type of ligand, the list of ligands will change accordingly. Similarly, after chosing a particular ligand, the preview image will update.

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    For monodentate or haptic ligands, click on a hydrogen atom to attach the new ligand.

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    Example of ammine ligand attached to an octahedral iron atom

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    For bidentate, tridentate, tetradentate, and hexadentate ligands, click on multiple hydrogen atoms and the ligand will be attached accordingly. For example for a tridentate ligand, click on three atoms in order. If you click on three sites in a line, but the tridentate ligand is a triangle, Avogadro will attach a “best fit.”

    -

    Iron bipyridine molecule

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    Ligands tab#

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    Type

    Specify the denticity or hapticity of the ligand.

    +

    The drop-down allows selection from a range of ligand denticities, including common bidentate, tridentate, tetradentate, and hexadentate ligands, as well as conjugated haptic ligands.

    +

    By choosing From Clipboard, a ligand that has been copied to the clipboard can be used. +For further details on creating ligands, see below.

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    Ligand

    Choose a specific ligand to be created.

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    The drop-down is used to choose a specific ligand. +Its contents will update based on the choice of Type. +Various common ligands are shown for easy access, but more can be selected from the library by choosing Other….

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    A preview of the selected ligand and its attachment point is shown below the drop-down.

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    For monodentate or haptic ligands, left-click on a hydrogen atom to attach the new ligand.

    +

    Example of ammine ligand attached to an octahedral iron atom

    +

    For bidentate, tridentate, tetradentate, and hexadentate ligands, one hydrogen atom must be left-clicked for each attachment point. +For example, for a tridentate ligand, click on three atoms in order. +If the shape of the sites chosen does not match the ligand template (e.g. three sites in a line are chosen, but the tridentate ligand is a triangle), Avogadro will attempt a “best fit”.

    +

    Iron bipyridine molecule

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    Groups tab#

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    Functional groups are similar to monodentate ligands in that they attach to a molecule through one new bond, and there is some overlap in the available fragments.

    +

    However, the focus is on covalently bonded organic moieties.

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    Group

    Choose a functional group to be created.

    +

    The currently selected functional group can be changed by selecting from the drop-down menu. +Various common groups are shown for easy access, but more can be selected from the library by choosing Other…. +The library contains over 100 functional groups organized by element including sulfonates, acid anhydrides, boronic acids, and many more.

    +

    Selecting other functional groups in a dialog organized by element

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    A preview of the selected functional group and its attachment point is shown below the drop-down.

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    Attaching Functional Groups#

    -

    Functional groups are similar to monodentate ligands in that they attach to a molecule through one new bond.

    -

    Beyond the common choices, “Other…” includes a library of over 100 functional groups organized by element, e.g., sulfonates, acid anhydrides, boronic acids, etc.

    -

    Selecting other functional groups in a dialog organized by element

    -

    After selecting a group, a preview will appear. Click the “Insert” button and click on a hydrogen atom in the scene to attach the fragment of your choice.

    -

    Creating New Ligands#

    +

    Creating new ligands#

    While the ligand library includes many common ligands, you may wish to create your own or tweak a ligand before attachment.

    -

    As an example, we will build the salen ligand and add the attachment point for this tetradentate ligand. The process is similar for other ligands – Avogadro will use the location of a dummy atom (element zero) to determine where to attach to a metal or molecule.

    -

    After creating your ligand molecule, you should select the atoms which will be the attachement sites:

    -

    salen molecule with four selected atoms: two oxygen and two nitrogen

    -

    The Build ⇒ Add Centroid command will add a dummy atom at the center of the selected atoms:

    -

    menu indicating "Add Centroid" command

    -

    The ligand will now have a centroid dummy atom added. Draw bonds as desired to the attachment sites.

    -

    salen ligand with four selected atoms and new centroid dummy atom

    -

    The ligand can either be copied to the clipboard to insert via the Clipboard ligand type, or saved as CJSON to contribute to the fragment repository

    +

    An existing structure open in Avogadro can be easily turned into a ligand. +It could have been, for example, drawn by hand, or loaded from a calculation output file.

    +

    To demonstrate, we will build the salen ligand and add the attachment point for this tetradentate ligand using a dummy atom (an atom of element 0). +The process is similar for other ligands – Avogadro will use the location of a dummy atom to determine where to attach to a metal or molecule.

    +

    After creating your ligand molecule, select the atoms which will be the attachment sites:

    +

    salen molecule with four selected atoms: two oxygen and two nitrogen

    +

    The Build⇒Add Centroid command will add a dummy atom at the center of the selected atoms:

    +

    menu indicating "Add Centroid" command

    +

    The ligand will now have a centroid dummy atom added. +The dummy atom can be manipulated in the same way as any other atom. +Draw bonds as desired between the dummy atom and the attachment sites.

    +

    salen ligand with four selected atoms and new centroid dummy atom

    +

    The ligand can either be copied to the clipboard to allow insertion via the From Clipboard ligand type, or saved as CJSON to contribute to the fragment repository.

    -

    Creating New Haptic Ligands#

    +

    Creating new haptic ligands#

    Haptic ligands indicate bonding between a metal center and a delocalized pi system, such as an aromatic ligand.

    -

    As an example, we will build up an η4-cyclooctatetraene ligand. Either draw the molecule or use File ⇒ Import ⇒ Download by Name… to insert the basic molecule.

    -

    cyclooctatetraene molecule

    +

    As an example, we will build up an η4-cyclooctatetraene ligand. +Either draw the molecule or use File⇒Import⇒Download by Name… to insert the basic molecule.

    +

    cyclooctatetraene molecule

    Now select the four atoms to use for the haptic ligand:

    -

    cyclooctatetraene molecule indicating four selected carbon atoms

    -

    Now use the “Add Centroid” command to add a dummy atom at the centroid of the selected atoms. This is useful to create distinct hapticity (e.g., η3 cyclopentadienyl after selecting three carbon atoms instead of five):

    -

    cyclooctatetraene molecule indicating four selected carbon atoms and dummy attachment point

    -

    For a haptic ligand, we need one more dummy atom, perpendicular to the pi system. We can add an additional dummy atom perpendicular to the centroid:

    -

    Menu indicating "Add Perpendicular" item for haptic attachment points

    +

    cyclooctatetraene molecule indicating four selected carbon atoms

    +

    Now use the Build⇒Add Centroid command to add a dummy atom at the centroid of the selected atoms. +This is useful to create distinct hapticity (e.g. η3-cyclopentadienyl after selecting three carbon atoms instead of five):

    +

    cyclooctatetraene molecule indicating four selected carbon atoms and dummy attachment point

    +

    For a haptic ligand, we need one more dummy atom, perpendicular to the pi system. +We can add an additional dummy atom perpendicular to the centroid using the Build⇒Add Perpendicular command:

    +

    Menu indicating "Add Perpendicular" item for haptic attachment points

    After adding the perpendicular attachment, draw a bond between the centroid and the attachment site.

    -

    -

    You can either save this file as CJSON to contribute to the repository, or “Select None” to deselect all atoms and copy the ligand to insert into a new molecule.

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    +

    As before, you can either save this file as CJSON to contribute to the repository, or copy the ligand to the clipboard to insert into a new molecule.

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    Creating New Haptic Ligands

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    Selection Tool

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    Label Tool

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    Creating New Haptic Ligands

    diff --git a/docs/tutorials/drawing-simple-molecules.html b/docs/tutorials/drawing-simple-molecules.html new file mode 100644 index 00000000..eb94380f --- /dev/null +++ b/docs/tutorials/drawing-simple-molecules.html @@ -0,0 +1,674 @@ + + + + + + + + + + + Drawing Simple Molecules — Avogadro 1.99.0 documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    Drawing Simple Molecules#

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    First steps#

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    Left-clicking on the display will allow you to begin your journey into molecule creation. A left-click will create a carbon atom. A right-click will delete the atom.

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    Left-clicking the initial atom and dragging your mouse will create a bond to another carbon atom.

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    Avogadro uses carbon as the default element. A different element can be selected through the Element drop-down menu. +Typing the atomic symbol (e.g., O for Oxygen, As for Arsenic) is a shortcut for changing the selected element.

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    Water#

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    Let’s say you wanted to create water. You can either type in “O”, or select “Oxygen (8)” from the drop-down menu, and then click on the black display.

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    Left-clicking on an atom that has already been generated will also change the element. +In this case, clicking on the initial carbon atom changed it into an oxygen atom.

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    If the Adjust Hydrogens box is checked, hydrogen atoms in the molecule will be automatically adjusted to satisfy valency (as shown above).

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    Bond order is changed through the Bond Order drop-down menu, or by typing the numbers 1, 2, or 3. +Bonds are added by left-clicking on a bond that has already been created. Right-clicking on a bond deletes the bond.

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    Tip

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    New in 2.0 +The default bond order is “Automatic,” and will adjust with the length of the bond.

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    Carbon Dioxide#

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    Begin drawing the “O-C-O” structure. +After the skeleton is drawn, all you need to do is left-click on the bonds to make them into double bonds. +Left-clicking on the bonds will create a double bond (shown below).

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    Once you’ve created your molecule, you can optimize its geometry through the Extensions menu. +Selecting the Extensions menu, and clicking Optimize Geometry will provide your molecule with proper bond lengths and angles.

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  • Display Types
  • Extensions
  • Tutorials