Re: [phenixbb] on Cutting out density by Phenix

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 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 Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk