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. | ||
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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 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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