DeepView/Mutating Amino Acids: Difference between revisions
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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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