Alternate locations

Where the crystal shows a side chain in more than one conformation, choose the one to dock against.

A residue whose atoms have alternate locations is listed under its chain's altloc group, sorted into the usual categories. Clicking the altloc node itself highlights all of them at once, which is the quickest way to see whether any sits near your pocket, and whether you might want its side chain flexible in docking.

1FV1 Biomol 2, altloc group of chain D selected — **1FV1, Biomol 2, chain D, altloc node selected**: its three residues (SER'19, THR'83, THR'93) are highlighted in green.

Choosing a location

Each residue offers its locations, with their occupancies, as radio buttons in the params column. The chosen one is used for the receptor, and the others are left out.

SER19 of chain D with its two alternate locations — **SER'19 of chain D**: locations A and B, each at occupancy 0.50.

SER19 location A — Location A: the hydroxyl points elsewhere.

The choice is recorded in the receptor file (REMARK 850 AGFR altlocs D:SER:19:_ @A (0.50)), and it is applied in every tab that contains the residue.

The default

ADFR selects by default the location with the most atoms, then the one with the highest occupancy.

Ties are not reproducible. When two locations have the same occupancy, as all seven altloc residues of 1FV1 do, ADFR's pick depends on the order in which Python iterates a set. That order varies from run to run, so SER'19 defaults to A in some runs and to B in others. The same holds for agfr and AGFRgui. Ties are common (2 of the 20 altloc residues of 4A1X, 4 of 19 in 6BHG). If a tied residue matters for your docking, choose its location explicitly: the choice you make is always the one written.

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