Christopher wrote: >>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.
We will use lower case 'q' ... as in PyMol >>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. Good > 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". Jmol currently only chooses the first confirmation when multiple confirmations are present. > 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. I am not a chemist ... that was helpful ... thanks. > Thanks, > Christopher Bottoms > University of Missouri-Columbia I hope to implement this within the next few weeks. Miguel ------------------------------------------------------- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
