Missing side chains

Rebuild them from a rotamer library, check the rotamer in 3D, or keep only the atoms the experiment saw.

When some side-chain atoms of a standard amino acid are missing, ADapt lists the residue under sidechains to complete, with the atoms it will build (build: CG CD NE CZ NH1 NH2). By default each such side chain is rebuilt when the receptor is written: every rotamer of the library is scored for favourable contacts and clashes with its surroundings, and the best is used.

See the rotamer

1FV1 Biomol 2, ARG100 of chain D selected, with its rotamer preview — **1FV1, Biomol 2, chain D, ARG'100.** Selecting the residue centres the view on it and draws the side chain that would be built, with **cyan carbons**. The params column shows the rotamer, `auto 59`: the best-scoring of the library's 81 arginine rotamers. The status line gives its score: *Score: -1.0, contacts: 2 favorable 2 clashes*.

The drop-down lists every rotamer of the library. Choosing one redraws it and gives its score. You can also hover over the drop-down and turn the mouse wheel to step through the rotamers one by one, watching the preview and the score change:

rotamer 59 (auto) — **auto (59)**: score -1.0, 2 favourable contacts, 2 clashes.

**rotamer 3**: score -39.0, 6 favourable contacts, 7 clashes.

The drop-down is a preview. When the receptor is written, the side chain is built with the best-scoring rotamer (auto), whatever the drop-down shows. AGFRgui behaves the same way; the drop-down lets you judge the alternatives, not pick one.

Or keep the side chain as it is

Right-clicking a residue under sidechains to complete offers Complete sidechain (the default) and Include as is. The same menu on the category applies to all of its residues.

context menu on GLU158 of chain D — **GLU'158 of chain D**: its rebuilt side chain in cyan, and the right-click menu. *Include as is* keeps only the atoms in the file.

GLU158 marked use as is — After *Include as is*, the label reads `use as is missing: CG CD OE1 OE2`. The residue stays in the receptor with the atoms the file has, and its `REMARK 850 AGFR side chain completed` line is no longer written.

Completing a side chain far from the pocket changes little. Near the pocket it decides what the ligand will meet, so check the rotamer, or leave the side chain incomplete if its position is too uncertain to trust.

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