The shade in the 2D projection

[sapphire...@gmail.com]

Hi,

I use "e2project3d.py" to generate a stack of 2d images of one 3d object. But there is shade around the object in 2d images. I checked the program, it seems a "mask_gaussian" processor is used to generate 2d images. I have two questions for this problem.

1. How did you generate such shade? Is there any literature describing this processor in detail?

Though I read the "mask_gaussian" processor instruction on website, I am still confused with it.

2. Is there any program can help me generate 2d projections without shade?

Best,

Huiya

[Steve Ludtke]

It is useful to post an image documenting such problems, otherwise there is some ambiguity in what you are seeing. You would normally want to have the solvent density set to zero (regardless of whether there is real solvent or it's a model with vacuum 'solvent'. So, before running e2project3d:

e2proc3d.py map.hdf map.hdf --process normalize.edgemean

or something similar.

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

--
--
----------------------------------------------------------------------------------------------
You received this message because you are subscribed to the Google
Groups "EMAN2" group.
To post to this group, send email to em...@googlegroups.com
To unsubscribe from this group, send email to eman2+un...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/eman2

---
You received this message because you are subscribed to the Google Groups "EMAN2" group.
To unsubscribe from this group and stop receiving emails from it, send an email to eman2+un...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Sapphire Zhou]

Hi Steven,

This is the code:

real3d = test_image_3d(1)

real3d.process_inplace("normalize.edgemean")

sym = Symmetries.get("c1")   #The symmetric type of the particle

orients = sym.gen_orientations("eman",{"delta":30}) ## Generate 100 gen_orientations operator

proj2d = [real3d.project("standard",t) for t in orients] ## All projections

This is the test 3d image:

This is the projections:

Actually, the projection of the 3d density should  only contain 5 circles. But from the projections, we can see there are some shadow except for 5 circles. I would like to know some details about how did you add the shadow (or noise) to the projections. Can I get the projections without the shadow (noise).

Best,

Huiya

[Paul Penczek]

This is likely due to the truncation of Fourier series. Otherwise the pictures seem to be correct. 

Regards,

Pawel

On Apr 11, 2019, at 10:34 PM, Sapphire Zhou <sapphire...@gmail.com> wrote:

Hi Steven,

This is the code:

real3d = test_image_3d(1)

real3d.process_inplace("normalize.edgemean")

sym = Symmetries.get("c1")   #The symmetric type of the particle

orients = sym.gen_orientations("eman",{"delta":30}) ## Generate 100 gen_orientations operator

proj2d = [real3d.project("standard",t) for t in orients] ## All projections

This is the test 3d image:

<Screen Shot 2019-04-11 at 22.25.59.png>

This is the projections:

<Screen Shot 2019-04-11 at 22.26.56.png>

[Steve Ludtke]

Hi Sapphire,

this is why it's important to ask the full question.  You are misunderstanding what test_image_3d(1) is producing. It is not just the localized balls you see in the isosurface view, it is actually a fairly complex function varying in 3-D. If you use a 2-D (slice by slice) density display of the 3-D volume, you will see that the function contains all of the features you're seeing in the projections. It has nothing to due with the Fourier truncation Pawel suggested.  The projections you are making are simple sums in real-space, and they are completely accurate representations of the volume.

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

On Apr 11, 2019, at 10:34 PM, Sapphire Zhou <sapphire...@gmail.com> wrote:

real3d = test_image_3d(1)