DeepView/Mutating Amino Acids: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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-''If you can find the residue you want to mutate by inspecting the structure, you can skip this step.'' If the Control Panel window is not showing, use the Window menu to open it. This allows you to see the sequences of the protein chains. Hold down the shift key and click in the column "show" -- the molecule should disappear. Find the residue you wish to mutate, and click in the "show" column to make just that one residue appear.
+''If you can find the residue you want to mutate by inspecting the structure, you can skip this step.'' If the Control Panel window is not showing, use the Window menu to open it. This allows you to see the sequences of the protein chains. Find the residue of interest in the list in the Control Panel. Click the checkmark in the "show" column while watching the model. You should see the residue of interest disappearing and reappearing. Rotate the molecule to position the residue of interest for a clear view.
+:Surface residues are easiest to see. If the residue of interest is buried, you may use the Display menu to turn on Slab. Move the slab plane by holding down the shift key while dragging the mouse up and down.
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-Click on the residue you want to mutate, and a menu of the 20 amino acids will open. Release the mouse button and slide the mouse away from the menu, and the current amino acid will be highlighted. Click on the target amino acid for the mutation of this residue -- the new sidechain appears immediately!
+Click on the residue you want to mutate, and a menu of the 20 amino acids will open. Release the mouse button and slide the mouse away from the menu, and the current amino acid will be highlighted (highlight not seen in OS X). Click on the target amino acid for the mutation of this residue -- the new sidechain appears immediately!
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+Notice the rotamer message in red that appears just below the top row of large square buttons.
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+There are a number of possible conformations of the mutated sidechain, called "rotamers". Automatically, a rotamer has been selected with the lowest energy (fewest collisions and most favorable hydrogen bonds, if any).
+Following "R" are numbers such as 2/7, meaning that there are 7 possible rotamers for this amino acid, and the second has been selected automatically.
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+There may be several rotamer positions with equally low energy. Notice the score following "s:". Negative scores are favorable and positive scores are unfavorable. Click on one of the small triangles near the red rotamer message to step through the possible rotamers, noting the energy score for each one. As you do this, notice the green and pink dotted lines, which represent favorable hydrogen bonds or unfavorable steric collisions, respectively. Choose any one of the lowest energy rotamers that you prefer.
+:If you have Slab on, some of the green or pink lines may be hidden because they are outside the slab. Hold down Shift while dragging the mouse up and down to move the slab plane.
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+You may also wish to take into account the probability (value following "p:") of each rotamer for the secondary structure in which the mutated residue occurs.
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+Click the "Mutate" button again, and either accept or discard the mutation.
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+If you used the identification button to label the residue, the label does not change to reflect a mutation. Open the "Display" menu, select "Labels" and click on "Clear User Labels".
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+Use the File menu to Save Current Layer (the one Layer you have loaded). This saves a PDB file that you can use in [[FirstGlance in Jmol]] or other software packages.
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