generate 3d mask of ellipsoid shape

[kmani]

Hi,

How to make a 3d mask of ellipsoid in EMAN2?

thanks

with kind regards

Mani.

[Paul Penczek]

from sparx import *

g = model_gauss(sigmax, nx, ny, nz)

see:

http://sparx-em.org/sparxwiki/model_gauss

---

From: kmani <manikandan....@gmail.com>
To: em...@googlegroups.com
Sent: Tuesday, August 20, 2013 8:23 AM
Subject: [EMAN2] generate 3d mask of ellipsoid shape

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[Ludtke Steven]

In EMAN2 parlance, you can use the

mask.gaussian.nonuniform processor, eg:

e2proc3d.py map.hdf masked.hdf --process=mask.gaussian.nonuniform:radius_x=30:radius_y=20:radius_z=10

but this is a gaussian falloff, not a 'sharp' elliptical mask. Not sure what Pawel's response does either...

Can you clarify exactly what you're after ?

----------------------------------------------------------------------------

Steven Ludtke, Ph.D.

Professor, Dept of Biochemistry and Mol. Biol.         (www.bcm.edu/biochem)

Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu)

Co-Director CIBR Center                          (www.bcm.edu/research/cibr)

Baylor College of Medicine                             

slu...@bcm.edu

[Manikandan Karuppasamy]

Hi Stefen,

We would like to make a 3d (binary) mask of ellipsoid shape for refinement purpose. Our molecule is elongated in one direction (and a spherical mask includes more noise in other two directions).

with kind regards

Mani.

[Ludtke Steven]

Hi. Are you refining in EMAN2 or SPARX ?   EMAN2's refinement script intentionally lacks an option to impose a specific binary mask during refinement.

Rather, EMAN2 makes use of autogenerated masks based on the shape of your particle, rather than geometric masks (spheres, ellipsoids, etc.). A "hard" mask (one that goes suddenly from 1.0 to 0.0) can induce significant model/noise bias, and exaggerate resolutions (due to mask correlation effects). The automask EMAN2 generates has a soft edge, which limits the effect of mask correlation and bias, and is generated directly from the data in each iteration. The new e2refine_easy.py refinement strategy in the pre-release of 2.1 takes this a step further with 'gold standard' refinement (halves of the data set are refined completely independently). In any case, neither the old nor new refinement strategies permit the user to define a fixed mask of any shape.