[3dem] [EXTERNAL] focused refinement

[Montserrat Samso]

Dear Sonali,


I guess you mean a spherical mask. I am not familiar with dynamo but if t produces a binary mask, try creating a soft mask (for example using spider): this will emphasize the masked region without leaving out the densities outside the mask.


Best wishes,


Montserrat Samso, Ph.D.

Assistant Professor

Director, CryoEM Facility

Dept. Physiology and Biophysics

Virginia Commonwealth University

1101 E. Marshall St., RM 3-009

Richmond, VA 23298

Tel: (804) 828-8728

Fax: (804) 828-8492

E-mail: Montserrat.Samso at vcuhealth.org



________________________________
From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Sonali Dhindwal <sdhindwal at ccny.cuny.edu>
Sent: Tuesday, December 26, 2017 9:14:23 AM
To: 3dem at ncmir.ucsd.edu
Subject: [EXTERNAL] [3dem] focused refinement


Dear All,


I have a query regarding focused refinement.

I have a complex that I am trying to refine using Class3D and Refine3D  module in relion.

Due to the possible heterogeneity in positioning of these interacting partner with respect to each other, I have created a circular mask using dynamo and using it in relion to mask one of the interacting partner, so that the refinement focuses on it not the other interacting partner. ​But in doing so, it just chops the region outside the mask.


Please guide, how to create mask so that refinement program just put less weight on the structure outside the mask and not removing it and do refinement on the structure focusing in the inside of mask.​


Thanks and Regards

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