5.02.1 Chemical Sketcher Widget
Posted by Katrina Vuong on 17 June 2018 05:36 PM
This is the Chemical Sketcher widget. You can use it to draw bond-line representations of molecules and molecular reactions.
Drawing a Structure
You can draw a structure atom by atom using the Point-Drawing tool. Any atom of any element can be placed on the canvas with this tool.
To change the element selected, open the
You can also draw bonds between atoms with this tool.
The bonds themselves can be modified with the bond line tool, shown here.
To modify the charge on
You can quickly build more complex structures by using additional tools available
Using the Carbon Chain tool, you can quickly construct a hydrocarbon chain with as many carbons as you can fit in the canvas.
Using the Cyclic Builder, you can quickly add cyclopentane, cyclohexane, and benzene rings right onto the canvas. You can then add more fused rings if you wish, or use other structure editing tools to modify the rings as needed.
Using the Templates Database, you can add entire named structures quickly to the canvas. A number of structures are already available to you and are organized into separate chemical categories.
In addition to the above tools, you can save entire molecular structures to your local hard drive and re-load them to the Chemical Sketcher Widget canvas later using the Save MOL file and Load MOL file tools. See information on how to import and export MOL files below.
Drawing a Reaction
Once you have drawn your structures, there are a variety of other tools you can use to help annotate your structures and construct a cohesive representation of a chemical reaction. These tools include the Text Annotator, the arrow tool, the Flip Structure tools, and the Copy/Paste Structure tools.
Using the Text annotator, you can label structures, describe reaction conditions, and do any other number of things that can be shown in linear text.
You can also write some chemical formula (eg ‘C6H12O6’). When you do this, the text will automatically format itself with the proper subscripts (in this case ‘C6H12O6’ becomes ‘C6H12O6’).
Using the Arrow Tool, you can draw arrows of several different types to help represent the different steps of your reaction. Many types of arrows, including curved arrows, straight arrows, equilibrium arrows, single electron, and electron pair arrows are available.
Using the Cut/Copy/Paste structure tools, you can more easily move and replicate structures. You can quickly add many copies of the same structure if needed.
Searching Chemical Structures
See this article [link to Chem searching] to learn more about how to Search Chemical Structures contained in Widgets or attachment entries.
It is possible to import
.MOL files are a fairly standard way to represent molecules. Although there are other common file types, most chemical programs can
In LabArchives, you can follow these steps to import a MOL file:1. Copy the .mol file to the clipboard. Here is an example of a MOL file:
2. In the "Add Entry," toolbar click Widget. It can also be under the "More" option & select the Chemical Sketcher widget.
3. Click the folder icon to open the Load Molecule dialog window. See below for elaboration
4. Paste the MOL file into the dialog screen.
5. Click the "Load" button.6. The Chemical Sketcher will convert
If you create a molecule in LabArchives using the Chemical Sketcher widget and want to use it in another program,
Embed an image into your notebook
If you want to embed a molecule image into the Rich Text Editor (RTE), one of the most reliable ways to do this is to take a screenshot, then use local image editing software (Microsoft Paint or equivalent) to crop out the molecule from the screen capture, then copy/paste into your Rich Text entry.