Hey Pavel, Thank you for your thoughtful comments and excellent references.
I also just realized I made a mistake in an earlier message. When you "integrate" a map using its average value you want to multiply by the volume of the asymmetric unit, not the volume of the unit cell. If you multiply by the cell volume you are integrating over the symmetry mates as well. You probably just want to know the number of electrons in one blob (one ASU).
One quick response to Pavel's first comment below too. On 8/22/2022 9:48 PM, Pavel Afonine wrote:
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!
Not so! Unless the map is completely featureless there is always a highest point. That is where you put the first atom. Once placed, you subtract (or otherwise remove) the density of that atom from the map. In this new, modified, map somewhere else is now the new highest point. This is where you put atom #2. Etc. With each iteration you transfer density from the map into a model. I've tried to adopt a strategy that keeps the total number of electrons (model + map) fixed, but that creates some interesting problems. The trick is that as you remove positive density you don't want to introduce negative density. And by "negative" I mean dipping below the vacuum level. This vacuum level may seem arbitrary at first, but in the calculated map it is a very real thing that cannot be neglected. No amount of adjustment in xyz, occupancy or B factor can generate a negative peak in the calculated map. In a way, this positivity constraint is another reason why occupancy refinement is a good way to integrate density.
Truth be told, although my "divot" approach seems to work fairly well, I'm still not entirely happy with it. The general problem of finding a minimally complex constellation of atoms that explain a given blob I don't think is solved. But I imagine this would make for a good AI project?
Cheers, -James Holton MAD Scientist ######################################################################## 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/
