Hi Maia,

Now that Randy sent you a reference about the effect of very weak reflections will you include the changes in the refiment procedure?

My question was rather to satisfy my curiosity and not to convince me that removing of data is harmless (thanks Randy for pointing out that paper!). It is pretty obvious that removing any data is bad. It is in my to-do list to add intensity based ML target, but the users should do the right job from the start as well, by not setting negative intensities to zero amplitudes when at refinement stage you can't do anything good with those.

I am wondering about that because I get different maps from the phenix refinement and from the refmac refinement.

I guess you need to make sure which maps you are looking at, taht is make sure you compare apples with apples and not with oranges. phenix.refine outputs various maps, namely with and w/o filling missing Fobs, it rejects Fobs outliers (according to Randy's paper as implemented by Peter Zwart), it may or may not include test reflections into map calculations, and does a whole lot of other things that are different from any other refinement program.
If you have a specific problem case that I can reproduce, I would appreciate if you send it to me, so I do analyze it, and improve software if turns out to be necessary.

In one case I see the isoalloxazine ring of the FAD cofactor flat, in the other case this ring is bent. The same story with the densities for ligands. Is it about geometry restraints or effects of exclusion of very weak reflections?

Compare regular and missing-Fobs-filled maps for these regions (phenix.refine outputs both): are they different?

Pavel.