warning occurred when using e2proc2d.py to convert movie mode .dm4 files to .mrcs files

[jli...@stanford.edu]

Hi, 

I am new to EM filed. I am trying to convert a set of negative stain images in eman2.21. The images are movie mode .dm4 files and I used e2proc2d.py *.dm4 @.mrcs to convert the files to mrcs so that I could use them in relion. During the converting, it keeps giving me warning messages for each of the image that is under process:

Warning: sigma = 0 for image  33

Use the writejunk option to force writing this image to disk

I am wondering what causes it and will the warning matters for the following process. 

Thank you very much. 

Jing Liu

[Steve Ludtke]

That message implies that one or more images in the movie stack is empty (constant value in all of the pixels). if you use e2display.py to look at the movie stacks on the screen, do they look ok.

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

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[Jing Liu]

Hi Ludtke,

Thanks for your reply. Yes, it looks like there are some problems with the images. I could not open any of the images I transferred to the  cluster. I opened 4 images from my external drive locally, 3 of the stack images look fine and one of them have plenty of the images that are purely dark. I am not quite sure what cause the problem.

Thank you.

Jing

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From: em...@googlegroups.com <em...@googlegroups.com> on behalf of Steve Ludtke <slud...@gmail.com>
Sent: Tuesday, August 14, 2018 2:54:23 PM
To: em...@googlegroups.com
Subject: Re: [EMAN2] warning occurred when using e2proc2d.py to convert movie mode .dm4 files to .mrcs files

 

[Steve Ludtke]

What tool/method did you use for the cluster transfer?  I would suggest just trying the transfer again. If the tool you are using has a "text file" option, make sure it's disabled.

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