I too use the scroll wheel quite a lot when exploring a map. I just like to be grounded by the knowledge of what contour level I'm looking at so I can make estimations of physical interpretations as I'm going.

Is this peak likely a Zinc atom? A water molecule? Something at partial occupancy?

I can't tell at all from the appearance of the peak, but if I know the contour level on a physically relevant scale (not a statistically relevant scale) I can have a feel for what I'm looking at. I believe that is valuable information to add to that of the surrounding chemical environment and leads me to an interpretation that refinement is likely to support. I find that I'm much less likely to build a Zinc atom into that "strong" difference map peak only to be rewarded with a huge negative peak after refinement because the peak could only support a Zinc at 10% occupancy.

Sure, look at your map with a low contour level -- Just be aware that you are looking at a low contoured map.

Dale Tronrud

On 5/3/2022 6:32 AM, Paul Emsley wrote:
On 02/05/2022 20:19, Dale Tronrud wrote:

     When I watch people model building I see many scrolling the contour level up and down without regard for the numeric value of the level, apparently just choosing a value that makes the peaks appear the way they prefer the peaks to appear.


I recall a few years ago that Alex McPherson asked me how I chose the contour level and I said more or less this. He didn't like my answer :-).


This way of choosing a contour level seems dangerous to me as it seems to bias the appearance of the map towards the modeler's expectation.



I don't choose one level and don't recommend that others do so - the continuous re-contouring allow one to get a feel for where the signal descends into noise - so I am scrolling very frequently when deciding where a side-chain should go. I hum the Rawhide theme tune as I do so.


Paul.

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