Hi,
What happens if you specify "--o lowpass_filtered.mrcs" instead of "--o
lowpass_filtered"?
This should put all particles into one big MRCS file
"lowpass_filtered.mrcs" and
write a star file called "lowpass_filtered.mrcs.star".
(Yes, the message from the program is very confusing; I will fix it
once you confirm the program does what you want).
Best regards,
Takanori Nakane
> Hello all,
>
> Using RELION 3.0 beta, I am low-pass filtering a particles.star file of
> particles from a class average using:
>
>
> $relion_image_handler --i class_average_particles.star --o
> low_passfiltered --lowpass 15
>
>
> The first particle called in the class_average_particles.star file is the
> third particle of a stack:
>
>
>
> [log in to unmask]
>
> But, I get the following error when I try to use this new
> particles_low_passfiltered.star file
>
>
> $relion_image_handler --i particles_low_passfiltered.star --o test
>
> ==================
>
> ERROR:
>
> readMRC: Image number 3 exceeds stack size 2 of image
> [log in to unmask]
>
> The new .mrcs stacks are one image short and I believe it is dropping the
> first image from the stacks.
>
>
> $ e2iminfo.py Extract/job071/raw_data/00018_low_passfiltered.mrcs
>
> Extract/job071/raw_data/00018_low_passfiltered.mrcs 2 images in MRC
> format 400 x 400
>
> 2 total images
>
> This doesn’t occur in when I just read in the 00018.mrcs file and filter al
> l the images in the stack. (I believe this was a bug in RELION 2.1.0)
>
>
> $relion_image_handler --i Extract/job071/raw_data/00018.mrcs --o
> low_passfiltered_00018.mrcs --lowpass 15
>
>
> $e2iminfo.py Extract/job071/raw_data/00018.mrcs
>
> Extract/job071/raw_data/00018.mrcs 7 images in MRC format 400 x
> 400
>
> 7 total images
>
>
>
> $e2iminfo.py low_passfiltered_000018.mrcs
>
> low_passfiltered_018.mrcs 7 images in MRC format 400 x 400
>
> 7 total images
>
> Is this to be expected when using a particles.star file as the input?
>
> Best,
> Lieza M Chan
>
> Postbaccalaureate Research Fellow
> National Institute of Diabetes and Digestive and Kidney Diseases
> National Institutes of Health
> email: [log in to unmask]
>
>
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