On Thu, 2010-07-15 at 15:42 -0700, Pavel Afonine wrote:
It is in todo list, but it doesn't have high priority. Frankly, I don't know how to do this cleanly - minimization with inequality constraint (as opposed to what we have no - minimization with strict constraint). I'm sure there are right methods for this, but it might turn into a few months project to accomplish for unclear gain.
Reset occupancies that are outside the [0,1] range at every step of minimization. Even better approach is to revert back to the previous step, fix the offending parameters at 0 or 1 and then minimize using the rest of the parameters. You can also try adding a steep penalty to the target function - this will allow occupancies to be a tiny bit outside the range during minimization but the offending parameters can be reset and fixed prior to the very last step. A cheaper trick would be to create a dummy atom that contributes nothing to Fc (just set its scattering factor to zero) and then add it to the group as a "sink". Others may come up with better ideas but I am not trying to compel anyone to actually implement anything, since it may turn into a few months project for me ;) Careful reading of my post shows no such requests, and in fact there is an alternative: latest version of refmac does allow refining occupancy for multiple conformers without constraining total occupancy to 1. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs