We will also add an operator to the label formatter so that this data can be output. label %o
neither '%o' nor '%O' are used yet.
Q: Do you want to use lowercase 'o' or uppercase 'O' ? (we would use the lowercase version unless we want to reserve it for some other atom property that is more popular)
The abbreviations I've seen (and used) for occupancy are "Q" (or "q"), or less commonly "Occ". For example, the programs CNS, XPLOR, and PyMol use upper and lower case "Q" for occupancy.
Q: If not, what is the range of possible value? Q: If I see a file that has spaces in this field, is the default value 1 ?
Its value can range from 0.00 to 1.00, but the default value would be 1.00.
I would also note that multiple conformations or partial occupancies can apply to ANY atom in a PDB file: ligands, solvent, backbone or side chain. Often solvent atoms modeled at partial occupancies don't have "alternate conformations". The density is simply too poor or too weak to warrant saying that the solvent atoms are always present at that particular position in the unit cell.
Thanks, Christopher Bottoms University of Missouri-Columbia
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