I think Joe has figured it out already. Trying a different program when the one you are using gives you trouble is a sure way to see if the problem lies with data (I assume that buster, cns, phenix, refmac and shelx all produce maps that resemble the same reality, and if positive density comes from data it will hopefully show up in all cases). As for metaphors, it's more like plugging the same video card in two computers to see if the problem is the card itself or the motherboard. IIUC, the kick maps are intended to reduce bias and maybe get one a better density in not-so-clear region. As far as well refined model regions go, calculating phases from a set of models with randomly shifted atoms seems to certain extent resemble increasing the B-factors. So the positive density that shows up first on the heavier and/or less disordered atoms seems like an expected outcome. Cheers, Ed. On Mon, 2010-12-20 at 21:43 -0800, Pavel Afonine wrote:
Refine with refmac and see if the positive density shows up there too. If it does, then either there is something peculiar about your structure or both programs suffer from the same bug that somehow only shows up with your particular dataset. If not, then it is indeed phenix bug (still rather specific to your dataset).
Although this may definitely give more clues, I see this way of debugging this problem more like treating the appendicitis with Tylenol -:) This may help in some way but will unlikely identify the problem and fix its root. Solving a puzzle like this typically involves reducing the amount of "variables" by simplifying the task that still results in problem rather than making it more complex to solve by involving more "variables". Oh, I guess you know what I mean by "variables" so I don't go into it.
All the best! Pavel.
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