On 12/10/2020 19:11, Paul Emsley wrote:
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).
I meant 0.1 or 0.01
Also the above presumes that you have pressed the "Estimate" button when
selecting the map weight. (Actually I often divide that number by 2 or
so - it doesn't make much difference but tightens up the final geometry
a bit).
As Rob says, it's a bit "trial an error" (where the trial lasts a few
seconds) - really I'm asking "is the protein moving like I want it to
move?" One cannot interactively change alpha (that might be a useful
thing to add to the refinement).
Paul
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