On 12/10/2020 13:44, Sorbhi Rathore wrote:
Dear all,
Could anyone please suggest the best way to decide which German-
McClure Alpha value to use during refinement (both at a higher
resolution and lower resolution areas for a cryo-EM map)?
I am using coot 0.9.1 pre EL(ccpem).
A carefully-worded question.
For cases, where the model doesn't initially fit the map:
In 0.9, there was the danger or tearing the protein apart with too much
yank and too much alpha (low weight). That's why I used to be
conservative - using an alpha of 0.03 or so (occasionally 0.1 or 0.001).
With proportional editing in 0.9.1, I find I yank less (instead, using
several micro yanks) and because the shift is distributed over a far
larger range and is ameliorated by distance from the yanked atom, I find
that protein either doesn't tear or usually re-anneals very pleasingly
even with a high alpha.
Proportional editing radius is changed by Ctrl-middle-mouse scroll.
For cases where the model more or less fits the map, I use 1 or (.3 or
10 (if I want to practically turn them off without deleting them))
Paul.
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