Cannot unstack .mrc file

[Anton Avramov]

Hi Steve, 

Could you help me with another issue. I have a .mrc tilt series file that I want to unstack, but I cannot figure out how to do that. 

Here is some info 

EMAN 2.99.47 ( GITHUB: 2023-03-04 13:31 - commit: 3f313008c3185410fe859663e763dffb9c0b6fcc )
Your EMAN2 is running on: Linux-3.10.0-1160.71.1.el7.x86_64-x86_64-with-glibc2.17 3.10.0-1160.71.1.el7.x86_64
Your Python version is: 3.9.16

I tried to use both e2proc2d and e2proc3d

e2proc2d.py ./Position_1.mrc ./pos1.mrc --unstacking

e2proc3d.py ./Position_1.mrc ./pos1.mrc --unstacking 

But all I get is a single file, which is twice as heavy and it is essentially the same tilt series. 

Do you know what I'm doing wrong? 

Thanks!!

Best, 

Anton 

[Ludtke, Steven J.]

The best strategy is actually to just rename the files .mrcs instead of .mrc. The contents of a stack file and a 3-D volume are identical in MRC format. There is no (reliable) way of identifying, so the community has generally adopted the convention that .mrcs filenames are for stack files and .mrc filenames are for 3-D volumes. Yes, e2proc2d/3d do have some stacking/unstacking mechanisms you can use for files where there is a difference (ie - HDF where you can have stacks of volumes, for example), but just using .mrcs is a much easier approach. Then EMAN2 will see it as a 2-D stack.

---

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

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[Anton Avramov]

Thank for the reply! 

I have a tilt series file that has 33 tilts, I want to unstack it to have 33 individual files and struggle to do so. Every time when I use e2proc2d\3d for unstacking I only get a single file. 

[Ludtke, Steven J.]

You renamed the file .mrcs and used e2proc2d.py?  There is no need/point in "unstacking" once it has the .mrcs filename. That is,

e2proc2d.py x.mrcs y.mrcs

will just copy the stack from one file to another, they will both be stacks. If you want separate files

e2proc2d.py x.mrcs y.mrc --unstacking

or 

e2proc2d.py x.mrc y.mrc --threed2twod --unstacking 

should both be viable approaches. What outputs do you get when doing this?

---

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/eman2/02d348f8-2b2f-499e-be0a-d2e83b3201bcn%40googlegroups.com.

[Anton Avramov]

Hi Steve, 

Yes, I renamed the file into .mrcs and used e2proc2d.py. My tilt stack is 33 tilts and I want to have separate file for each tilt. 

When I run e2proc2d.py x.mrcs y.mrc --unstacking I get a new y.mrc stack and not individual files. 

When I run e2proc2d.py x.mrc y.mrc --threed2twod --unstacking I get an error:  need 3D images to use this option. 

But, I figured that out while I was writing this message :)

If I rename my file back to .mrc and run e2proc2d.py x.mrc y.mrc --unstacking I get individual files! 

Thanks for your help! I unfortunately going to create another discussion soon regarding importing tomograms from IMOD. :)