additional instructions Lab 9 - Labeling proteins in CN3D 1...

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Unformatted text preview: Labeling proteins in CN3D. 1. Download the yqhd stated in the manual. 2. Once the file has been downloaded. Setup yqhd as stated in the manual. 3. The manual does not state how to label amino acids in your protein. Do the following things 1. Select your amino acid of interest. Lets say Glycine 38. You can go to the sequence window and pick glycine 38 of yqhd. Notice at the bottom left of the window shows you the position of the amino acid (Figure 1). As you move along the different amino acids, the number changes. NOTE: Use the number in the parenthesis (PDB 38). 2. Once you have selected the amino acid, go to Styles>Annotate. A new window will pop up and then click on New and a new window pop up. Now click on Edit Style and another window will pop up. Go to the Labels tab. Change the Spacing from 0 to 1. In the Spacing field, you will specify how many amino acids will be labeled again after the first label. 1 means that every amino acid will be specified, 2 means every other amino acid, and 3 will be every 3 amino acids will be labeled. Everything should look like Figure 2. 3. Change the Numbering from Sequential to PDB. Here your amino acid will be labeled based on original protein. 4. Apply all settings and you will see that Glycine 38 is now labeled. 5. You can now label the rest of the amino acids in the active site. 4. To do a printscreen, go to File and select Export PNG. Now you just saved an image of your labeled yqdh. Joseph Cao Labeling proteins in CN3D. Figure 1 Figure 2 Joseph Cao ...
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