Alternate locations
From Proteopedia
Some PDB files have alternate locations (altlocs) for some atoms. Each atom that has altlocs is marked with an altloc identifier, typically A and B. At sufficiently high resolution, two positions may be visible in the electron density map for certain atoms. If these have approximately equal densities, each alternate location will be assigned an occupancy of 50%. Sometimes 3 or even more alternate locations may be distinguished (see examples in the following section).
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Visualizing alternate locations
FirstGlance in Jmol tells you how many atoms have alternate locations (when you are in more details mode), and the range of occupancies assigned to them. It tabulates summaries of alternate locations and occupancies, with links that highlight subgroups. It can animate alternate locations. Examples:
- These links display the model in FirstGlance. Look in the Molecule Information Tab for alternate locations.
- Glu3 in 3HYD. The atom with the largest distance between its alternate locations is the sidechain epsilon oxygen 1 (OE1), with 1.66 Å between alternate locations. Here are its ATOM records from the PDB file. The vertical bar points to the column with the altloc A and B designators.
| X Y Z Occ Temp ATOM 49 OE1AGLU A 3 9.326 0.609 10.555 0.50 4.93 ATOM 50 OE1BGLU A 3 8.211 1.826 10.769 0.50 8.58
- 1BSZ: Arg155 in chain A has 3 sidechain positions, each given an occupancy of 33%.
Models with the most alternate locations
The OCA Database and Browser highlights the structure with the most 'altlocs'. See Believe It or Not! within Proteopedia for that Protein Data Bank entry and other information mined from OCA.
PDB Format
The altloc identifier occupies the 17th column for the ATOM records section of the PDB format.
CIF Format
In the mmCIF format correspondence may be 'alt_id'. However, because that is listed as corresponding to 'alt_loc' , it is unclear if that is the same as 'altLoc' listed in the PDB format guide.
