[phenixbb] on Cutting out density by Phenix

Randy Read rjr27 at cam.ac.uk
Thu Apr 23 00:33:12 PDT 2015

Dear Smith,

I suspect that you need to think a bit about whether the contour level you're using for the two maps is the same, in terms of electrons per cubic Angstrom.

Best wishes,

Randy Read

> On 23 Apr 2015, at 07:41, Smith Liu <smith_liu123 at 163.COM> wrote:
> Dear All,
> I have tried to cut out the density by the Phenix graphical interface with the cutout type as model, but I find in the cut out map, there is more density arond the residues than in the input mtz map, here I mean, take a Lys residue as an example, in the input map, from Calpha there is about 1/2 of the sidechain was surrounded by the density, but in the cutting out map, there is about 2/3 of the sidechain was surrounded by the density.
> Will you please tell me if I want to get the cutting out density in the model cutout type, how can I have the cutting out density looks exactly or very close to the input density in the input mtz?
> Smith
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Randy J. Read
Department of Haematology, University of Cambridge
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