volume extraction from the STA result

[Meng Zhang]

Dear eman2 developer

Can I have some guidance or detailed command examples for preparing training pair-3D volume after the e2tomo STA? I believe some eman2 commands can simply help to complete the task. specifically, I want to :

1. extract the highest score of 500 subvolumes from the particles3d folder based on my STA alignment result in spt_00/aliptcls3d_xx.lst (I used the e2spt_refine_new protocol), and converted them into individual mrc files.

2.  generate 500 ground truth volume mrc files by applying the corresponding trans-rot matrix in spt_00/aliptcls3d_xx.lst to the three_xx.hdf

Thanks in advance

Meng

[Ludtke, Steven J.]

On Feb 21, 2024, at 3:54 PM, Meng Zhang <zhangme...@gmail.com> wrote:

Dear eman2 developer

Can I have some guidance or detailed command examples for preparing training pair-3D volume after the e2tomo STA? I believe some eman2 commands can simply help to complete the task. specifically, I want to :

1. extract the highest score of 500 subvolumes from the particles3d folder based on my STA alignment result in spt_00/aliptcls3d_xx.lst (I used the e2spt_refine_new protocol), and converted them into individual mrc files.

You'd need to write a python program yourself to do this. We don't have any tools for selectively extracting particles based on their alignment results. For example (untested, but should be roughly right):

from EMAN2 import *

lsx=LSXFile("spt10/aliptcls3d_03.lst")

scr=[[lsx[i][2]["score"],i] for i in range(len(lsx))]

i=0

for s,n in sorted(scr)[:500]:

im=EMData("spt10/aliptcls3d_03.lst",n)

im.write_image(f"mrc_{i:03d}.mrc",0)

i+=1

2.  generate 500 ground truth volume mrc files by applying the corresponding trans-rot matrix in spt_00/aliptcls3d_xx.lst to the three_xx.hdf

from EMAN2 import *

lsx=LSXFile("spt10/aliptcls3d_03.lst")

scr=[[lsx[i][2]["score"],i] for i in range(len(lsx))]

i=0

for s,n in sorted(scr)[:500]:

im=EMData("spt10/aliptcls3d_03.lst",n)

im.process_inplace("xform",{"transform":im["xform.align3d"]})

im.write_image(f"mrc_{i:03d}.mrc",0)

i+=1

I'm not sure I'd call this "ground truth", though...

Thanks in advance

Meng

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Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 
Deputy Director, Advanced Technology Cores                  and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center

[Meng Zhang]

Thanks, Steven. Unfortunately, there is no e2proc3d.py function to complete these tasks, however, these commands are very helpful.

Regards;

Meng

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/363FAA9A-DB5D-4CE3-AD41-64D6DDFDB5A6%40bcm.edu.

[Ludtke, Steven J.]

Hi Meng,

that just isn't an operation most users would ever need to do...

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Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 
Deputy Director, Advanced Technology Cores                  and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CAPmS4-rqNwdPzX1CB9Km6Ry84Khjia_WEc2uQRQg-eUQcWBM%2Bw%40mail.gmail.com.