DeepView/Mutating Amino Acids: Difference between revisions
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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. | ''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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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. | 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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Use the File menu to Save the one Layer you have loaded. This saves a PDB file that you can use in [[FirstGlance in Jmol]] or other software packages. | 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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