Hi,
I hopefully fixed this problem in the latest commit (f00e071).
When the input is a STAR file and the outputs are multiple STAR files
(i.e. --o is not something.mrcs but a prefix), the output stack IDs
will be re-numbered. Could you please test this?
Best regards,
Takanori Nakane
On 2019/02/06 18:25, Chan, Lieza (NIH/NIDDK) [F] wrote:
> Hello,
>
> Yes, When I use "lowpass_filtered.mrcs" instead, then all the particles into one .mrcs file. I was planning on making individual MRCS files, but this will likely work. Is there any limit on the number of images that can be in a single MRCS file? If the particles.star file contains ~ 50,000 particles, will having that large of a MRCS file be an issue?
>
> Best,
> Lieza M Chan
>
> Postbaccalaureate Research Fellow
> National Institute of Diabetes and Digestive and Kidney Diseases
> National Institutes of Health
> Bldg 8, rm 1A03
> 8 Center Dr, Bethesda MD 20892
>
> email: [log in to unmask]
> phone: 301.827.3604 <tel:301.827.3604>
>
>
> On 2/6/19, 12:58 PM, "Takanori Nakane" <[log in to unmask]> wrote:
>
> 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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>
>
>
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