Solution for "ERROR: No images left to include after applying filters" problem

[Steve Ludtke]

We have been getting sporadic reports of a problem when building sets, getting:

ERROR: No images left to include after applying filters

And not having any sets/* files to continue processing.

Thanks to someone providing some data, I've managed to track down this problem. The issue was with projects with a very large A/pix value (which is why it generally happened with negative stain data).

In any case, a correction has been committed, so the 6/29/16 daily release will contain a fix.

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol. Those who do
Co-Director National Center For Macromolecular Imaging ARE
Baylor College of Medicine The converse
slu...@bcm.edu -or- ste...@alumni.caltech.edu also applies
http://ncmi.bcm.edu/~stevel

[Steven Ludtke]

Sorry, should have added that the workaround for older versions is to specify a slight negative value (-0.1 for example) for minhisnr when building sets. I believe doing this will completely avoid the problem.

The issue was with projects with an A/pix so large that no high resolution SSNR could be computed at all, leaving it at exactly 0. The inequality used for testing was ">", not ">=". So, if your A/pix was too big it could never satisfy the condition :^(

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

[ashuthe...@gmail.com]

Hi Steve,

I am getting the same error with a cryo em data. I tried specifying -0.1 value to minhisnr, still that doesn't help. Interestingly, I could successfully build particles with ~50K particles from the same data set.  However, when I tried building it with ~100K data, I get this error. A/pix for the images I am working on is 1.5.

EMAN 2.12 (CVS 2015/10/19 09:00:04)
Your EMAN2 is running on:  Linux-2.6.32-642.11.1.el6.x86_64-x86_64-with-redhat-6.8-Santiago 2.6.32-642.11.1.el6.x86_64 x86_64
Your Python version is:  2.7.3

The command I issued was:

e2buildsets.py --setname=my_stack --allparticles --minptcl=0 --minqual=0 --mindf=0.0 --maxdf=20.0 --minlosnr=0.0 --minhisnr=-0.1 --minbfactor=0.0 --maxbfactor=5000.0

I also saw in the mailing list that e2proclst.py could be used for this purpose to manually create the list. However, I could not figure out the syntax for this purpose.

Could you please help through this step.

Thanks a lot!

Ashu

[Steven Ludtke]

Could you post the exact error you're getting ob cryo data?  May be a problem  that is fixed in 2.2 (which is now gradually appearing on the download page)

Sent from my iPhone

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[ashuthe...@gmail.com]

Hi Steve,

The exact error was:

2942 particle stacks identified
Filtering by Defocus and B-factor
ERROR: No images left to include after applying filters!

Though, it is working now. I was  playing with parameters today. The images have been collected with defocus range of -2 to -4. In the json file I checked the calculated defocus range and it was well within -2 to -4. However, it was not building set with this defocus range. I tried -2 to -4, 0 - 20, 2 to 4. What eventually worked was -5 to +5. The complete particle set involving ~100K particles, excluding ~400 bad particles, could be built with this defocus range.

Then I looked back at the data set of ~50K particles, where I was expecting that it had worked. But it had included only 5000 particles out of 50,000 !

Guess, we need to give a broader range of defocus than what we actually have.

Thanks,
Ashu

[Steve Ludtke]

In EMAN2, underfocus is positive.  This seems to be the generally adopted convention nowadays. (In EMAN1 it was negative).

[Gábor Oroszlán]

Hi all,

I have the same issue now, do you have any guess what could go wrong? I attached a photo.

Best,

Gabor

[Ludtke, Steven J.]

Try midres instead of lowres and see what happens. Are you using EMAN2.91?

--------------------------------------------------------------------------------------
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)

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<20210716_155758.jpg>

[Gábor Oroszlán]

Hi Steve,

Thanks, I restarted. I believe yes, it is 2.91.

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