Hi Amy - happy to see that the increase in Laplacian threshold helped. See some more comments bellow comments.
> (1) As the threshold increases, more and more points are eliminated, because the Laplacian at these positions is less negative than the reference Laplacian (=threshold*min(Laplacian)). Is it right to think that the eliminated positions are likely the false positives where a solvent molecule should not be placed at?
You can think about these eliminated positions as corresponding to loosely bound waters. For ions, we sometimes use terms such as diffusely or territorially bound which is opposed to site-bound. By increasing the Laplacian threshold you are more likely to identify site-bound waters.
> (2) For the occupancy values, am I right in thinking that one can average the occupancy values by volume of the blob, or is there some way to get the individual occupancy value for each position in a blob?
>
That is a good question. The current code integrates over the entire volume of the blob and so if you wanted to approximate the occupancy for each water position you could divide it by the number of waters contained within the blob. I am planning to change this in the next version of the code and integrate the density around each water position.
I hope this make sense, let me know if I have answered your questions.
George Giambasu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Mar 28 2021 - 19:00:02 PDT
