Hi James, - Where exactly inside the blob of density do you place these dummy atoms? > > Where? At the peaks. >
Peaks? This means you need to have atomic resolution data and also blobs representing ordered atoms, so you actually have peaks! > What I usually do is pick peaks, put atoms at the highest ones, then > either refine for a bit or simply subtract a "divot" of density around each > added atom and then look for new peaks. Once the height of after-refinement > positive difference features drops to an insignificant level I stop. NB > that "significance" of any sigma level depends on the number of voxels in > the map, but its usually between 3.5 and 4.5 sigmas. > One can also start with a 3D "grid" of dummy atoms. Gaussians spaced > within 0.8*fwhm of each other form a pretty flat density profile. In such > cases refining just one overall B factor and individual occupancies with no > xyz motion is pretty effective all by itself. > Dummy atoms on a 3D grid approach in fact has a documented instance of a successful application (although in a slightly different context): "Local improvement of electron density maps". (1997). Acta Cryst., D53, 540-543. - I guess O or C as an atom type should do it, but what about B factor > (would you refine B as well?)? > > I find oxygen will do in peak-picking cases, but for grid atoms under very > smooth density and closely-spaced atoms I have found the individual > occupancies get rather small, the round-off error of occupancy from 0.01 to > 0.00 creates a granularity of ~0.1 electron, and this can start creating > artificial noise in the fit. For cases like this I have gone to "liquid > helium", or modelling dummy atoms as He. Yes, you might think that hydrogen > would be better, but H atoms have so many special checks and whiz-bangs for > how they are treated I eventually gave up and went to He. (One could also > argue that at low enough temperature He atoms are allowed to "overlap" > anyway. ;) ) > Yes, H (Acta Cryst. 1997. D53, 540-543) or O (Acta Cryst. 1993. D49, 129-147) depending on whether you do peak picking or refine DAs on the grid. And I see why He may be a better choice, yes, hydrogens are too special these days! Pavel ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
