Hi
I tried the TRPV1 dataset, and it worked fine on my machine, but when I want to upload my own data, I got an error message: “Relative paths are not specified in images, so data input must be a single file!” .
Here’s my .star file looks like:
data_
which will generate a stack with all your particles and a star file referencing it (although for some reason relion always adds an extra “mrcs” to the stack name). This is what I have been doing with no problems so far.
Looks like your star file is missing _rlnImageName. That field is what we use to read star files and know both where the corresponding mrc file for a given particle is, and also the index into that mrc file (_rlnImageName has a format like <image_idx>@<mrc_file>).
Oliver’s suggestions seems like a good way to generate a new star file that contains the necessary fields.
I have a related question. After the normal pre-processing procedures in relion, all particles are grouped per microscope image. Since I have hundreds, I just want to sweep them into one file and work with that.
Can you elaborate on the relion_preprocess method? I can’t get it to locate the correct input file (which you labeled data_in.star) I want it to locate a particles.star from the particle extraction.
The error:
MetaDataTable::read: File particles.star does not exists
Other thing I tried: Sweeping mrcs together can also be done with imod’s ‘newstack’, but then I don’t have a correct .star file obviously, because it refers to the initial filenames.
This should generate two files - particles_for_cryosparc.star, and particles_for_cryosparc.mrcs.mrcs (which you should rename to particles_for_cryosparc.mrcs).
The error you give indicates that relion can’t find your particles.star file - are you sure it is in the same dir where you are running relion_preprocess, or if not are you giving the appropriate relative path (e.g. Particles/particles.star)?
I indeed triple checked the relative path before (folder/subfolder/particles.star), but it seems I still did something wrong there. I have copied the particles.star into the relion folder and now it works.