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Unformatted text preview: rticular journal, there are many other matters to arrange during manuscript preparation. For this reason, Advanced Chemistry Development has included Instructions for Authors, a hyperlinked list of guidelines for over 80 journals. 1. For example, from the Help menu, choose Instructions for Authors. 2. Find the Journal of Organic Chemistry in the list. 3. Click the link to the Adobe PDF file to display the corresponding file. ACD/ChemSketch Tutorial 104 Working with Styles in Structure Mode 4. Click Contents to return to the list of other journals so you can view their guidelines too.
Note Not all journals have explicit instructions for structural drawings, and so they do not appear as a definite style listed in the Structure Properties dialog box. 11.3 Creating Your Own Style
Let’s say that you want to make a presentation in which you want to colorfully distinguish between the sugar, phosphate, and amino acid groups of the portion of DNA you are describing. 1. Open the file DNAFRAG.SK2 (or draw the DNA fragment shown above in Section 5.5.1) and make sure that you are in the Structure mode. 2. Switch to the Lasso On tool and click Select/Move . 3. Select the sugar components by dragging around them (hold down SHIFT when selecting separate components): +Shift 4. Point to any part of the selected fragment so that the selection squares become black. Double-click to display the Properties panel. ACD/ChemSketch Tutorial 105 Working with Styles in Structure Mode 11.3.1 User-defined Style: Sugar
Now we will define our own style for the sugar components: 1. In the Atom Style and Bond Style areas, specify the color for the selected fragments, for example, red. Set the bond width to a different value, for example, 1.9 pt. Units of measurement used in most of the panels within ACD/ChemSketch correspond to those set in the Preferences dialog box (Options menu). You may set values for width, length, etc. in points/inches/millimeters/centimeters. Type the values and add the unit you want (pt/in/mm/cm), e.g., 5 pt. The values will be recalculated in the corresponding units of measurement. 2. Click Apply. As you can see, the selected segments are colored with red now:
O OH HO P O O N
O Note NH O O O HO P O
O N O N N NH NH2 OH 3. To save this style for future use, in the Style box of the Properties dialog box, type Sugar and click Save: 4. You will be prompted whether you want to save this user-defined style. Click Yes. ACD/ChemSketch Tutorial 106 Working with Styles in Structure Mode 11.3.2 User-defined Style: Phosphate
In this section, we will define our own style for the phosphate components: 1. Similarly, select the phosphate part of the structure, and define a thick bond width and blue color for the bonds and atom fonts. 2. Save this style as Phosphate and then click Apply to apply it to the structure:
O OH HO P O O N O O O HO P O O O N N NH2 N O NH NH OH 11.3.3 User-defined Style: Base
We can also define our own style for the bases: 1. For the bases, set the color of the atom symbols to dark green and the bonds to neon green. 2. Save this style as Base and then click Apply to apply it to the structure:
NH HO P O O
N O O
O O HO P O O O N NH N N NH2 OH ACD/ChemSketch Tutorial 107 Working with Styles in Structure Mode 11.3.4 User-defined Style: Highlight
Perhaps, during the course of your presentation you want to draw the attention of the audience to the oxygen atoms. We will create a fourth style, Highlight, for this. 1. Use SHIFT+ click to select the oxygen atoms indicated below with the arrows: 2. Double-click any of the selected atoms, and, on the Properties panel, switch to the Atom tab. 3. To change the color and size of both the atom symbol (oxygen in this case) and hydrogen, click the corresponding buttons in the row below the preview area holding down SHIFT. You may also change other atom attributes (hydrogen index, charge, valence, isotope, numbering) by clicking the corresponding buttons. 4. Change the color, atom size, and other attributes, for example, to the following settings: Note Note In a similar manner, you may change the bond attributes. ACD/ChemSketch Tutorial 108 Working with Styles in Structure Mode 5. Click Apply to obtain the following structure:
HO P O
N NH O O O
HO P O N NH O N N NH2 O OH 6. Save the style as Highlight. 11.4 Applying Existing Styles
To practice applying the styles you have just created, open DNAFRAG2.SK2. 1. Use the Lasso tool to select the five-membered sugars as shown in Section 11.3. 2. Double-click those substructure fragments or from the Tools menu, choose Structure Properties. 3. On the Properties panel that appears, from the Styles box, choose Sugar: 4. Click Apply. The chosen style will be applied to the selected structure or fragment. 5. Choose the phosphate groups. From the Style list, choose Phosphate. Click Apply. 6. Similarly, select the two bases in the DNA fragment and click Apply for the Base style.
Tip The information about a user-defined style is stored on your local hard drive in the private directory that is specifi...
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