ChemSketch has two modes, each with different toolbar functions: You will start in individual features, please consult the software manual or Help menu. ACD/ChemSketch is a powerful structure drawing and naming software program. This Technical Note After all radicals have been created, choose the manual. Introduction to ChemSketch. ChemSketch is a free download for educational use. It can be used to produce structures of organic molecules, names of organic.
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Drawing Structures with ChemSketch. It is amazing that ChemSketch is freeware because it is a quite powerful chemical structure drawing program. One of its few drawbacks is that it is somewhat complicated to learn.
Draw any molecule and dock it flexibly to any protein with coordinates known
However, if you have any experience with drawing programs then some aspects of it should be easier for you to learn. Finally, you’ll see an interactive screen for Structure mode. Whenever you click on some part of the screen picture, you get help on that particular part. Keep the Help window open while you learn. You can get the same interactive help for Drawing mode.
Chemsketch has two modes: There are similarities and differences between them. Generally, the Structure mode generates structural parts of the file such as atoms and bonds and the Draw mode allows you to enhance them with arrows, boxes, and non-structure drawings.
In both modes, there are drop down dialog boxes and panels in which you make stylistic choices among different fonts, line widths, etc. As you explore the toolbar buttons, point to a button and in a moment a tool tip will appear. This is one of the best ways to learn the tools buttons and their functions.
When you are using Help, open the window on Mouse Commands. Each tool seems to behave slightly differently depending on whether you single or double-click, drag, etc. It is good to be aware of the possibilities. The two images below show the Structure and Drawing Modes windows.
In addition to the buttons in both modes, there are tool panels that apply formatting to your structure and drawing. Access the panels from the Tools menu in both modes. Tools Structure Properties in Structure mode.
The Structure Properties panel is open. The panel can be moved anywhere, on or off the main window. The two most commonly used tabs are “Common” and “Atom”. Tools Panels in Manul Mode.
Drawing structures — The best way to learn how to draw with ChemSketch is to start copying examples you see in books. There are some suggestions below you can copy for practice.
Use the Clean Structure tool to fix your drawing or sometimes it messes chensketch up. There are multiple levels of “undo”.
Drawing Tools and Objects. Drawing — Some of the tools here are more obvious in how they are used, but they are also of less chemical importance. Again, practice copying examples. You’ll find that your drawings are much easier to manipulate if you learn about Grouping and Ungrouping objects in Draw mode.
A great xhemsketch and a strong feature of ChemSketch are the Templatesthat contain pre-drawn structures and figures. Access the various templates from the drop-down menu or from the tool bars at the top and right side of the Structure Mode window. The Table of Radicals contains the commonly drawn monocyclic rings and small substituent and functional groups as well as amino acids.
The Template Window and Organizer is an extensive collection of structures and drawings organized by type, such as sugars, steroids, etc. When you open the Template Window, there is a menu of collections on the left, but clicking on the chmsketch box will reveal many more. You can choose your own short-cut menu in the Organizer.
Open the Templates Window and the Organizer to see what is available. You might start by exploring and checking these topics in the Template Window: Make sure you notice the little icon that indicates more than one page for many of these templates. Check out these Tools: Saving Files as Images. ChemSketch can save Export to these same formats as well as to bmp and gif files. When you export to gif format, for example, from a ChemSketch document that has multiple pages, only the page on view or the selected portion is saved as a graphic.
Each page in CS must be saved separately. You can copy a structure and maunal objects and paste it in another application such as Word or Excel.
What is the difference between the ways in which a structure and text are edited in Word after pasting? If you copy the image to Paint, or other graphics program, you can then save the file in the.
ChemSketch – An Introductory Guide
You can copy from other applications and paste into ChemSketch. If you want to open the 3-D file in another molecular viewer, save the file as an MDL. Embedding ChemSketch drawings in Windows applications. The last section of the documentincludes instructions on embedding ChemSketch drawings into Office apps. OLE is the next topic in the course.
Reproduce the structures shown in the Practice pages linked below. Drawing each of the practice structures will help you learn some of the features of ChemSketch, e. If you need to know how to do something, open Help.
Many times you will have to expand a collapsed structural formula and show the correct sterochemistry and geometry. This would be a good time to review hybridizationgeometrybond anglesnon – bonding electronsformal chargesetc. Here are a few e xamples, with answers. Select a ChemSketch object in the ChemSketch window. Embed it into a Word page using Paste and then Paste Special Is there any difference between the two methods?
Can you Link the ChemSketch object? Choose Insert Object in Word. Draw an object and finish embedding in Word. What do you do if you choose Create From File? Can you Link the file? Insert an equation into a ChemSketch document using Equation Editor.
Can you embed a Word document inside a ChemSketch document? If you can embed these objects, and you want to edit them, do you need to be in the Structure or Draw modes, or either?
The string can be read by chemsketchh humans and computers — computers cannot typically read the two- and three-dimensional structures generated by chemists. An individual element is represented by a standard atomic symbol. It is required to be present for each atom, except Hydrogen. Elements in the following “organic subset” typically have well-defined valences and may be written without brackets if the number of attached hydrogens conforms to the lowest normal valence consistent with explicit bonds.
This subset, and their lowest normal valences, are: Alternatively, sp2-hybridized atoms may be represented in lower case. Single bonds may be omitted.
If an atom is enclosed in brackets, all explicit Hydrogens must be shown, as in the last example for ethane, below. Branches are specified by enclosing them in parentheses, and can be nested or stacked.
The connection to a parenthesized branch is to the left. There is no need for brackets, charges, aromatic specifications, etc. In cnemsketch the rules for the language are basically:. ChemSketch is not only a molecular drawing program, it is also a molecular visualization program. You can toggle back and forth between the two programs.
To switch to the 3D window from the ChemSketch window: A good procedure for visualizing a molecule in 3D while preserving your drawing in the sketch pad is to first draw the molecule in Structure mode, then press the [ Copy to 3D ] button. The view switches to 3D and chemskehch molecule appears in the window. It is still a 2D object, however.
In the example shown here for butane, the program adds the hydrogens and adjusts the bond angles. If you rotate the molecule, you can see the anti staggered arrangement of the C-H bonds. The program has adjusted the geometry of the 2D sketch to the lowest energy molecular conformation anti staggered.
Place a cyclohexane chair structure from the Templates window into the ChemSketch window. Repeat the process described for butane, above. Be sure to rotate the optimized cyclohexane structure in the 3D window. What conformation is this? You can 3D-optimize your drawing in the sketch window before copying to 3D. However, you lose your original drawing in the sketch pad.