File and Directory Structure

CryoLike’s wrapper functions expect certain input and output files to be located on the filesystem in predictable locations. Most wrappers provide an optional prefix to determine the root directory, but within that root, the following expectations will hold.

Template Creation Patterns

See also Make templates from cryo-EM maps or atomic models

Inputs

Templates are generated from 3D structures in either PDB or mrc formats. Users are expected to pass a full valid path to any input files as part of the input list.

Outputs

Prefix set by the folder_output parameter.

Assume:

  • folder_output is FOLDER_OUTPUT

  • NAME is:

    • for files: the base name of a file, e.g. “file” for “files/file.pdb”

    • for in-memory arrays: templates_fourier_tensor_N where N is the number of that element in the input list

Generated template files will be written as:

  • FOLDER_OUTPUT/templates/templates_fourier_NAME.pt

  • FOLDER_OUTPUT/templates/templates_fourier_NAME_1.pt if that file exists (counter will keep incrementing)

  • FOLDER_OUTPUT/templates/template_file_list.npy for the list of files written

If plots are requested, they will be placed in:

  • FOLDER_OUTPUT/plots/templates_fourier_NAME.png

  • FOLDER_OUTPUT/plots/templates_phys_NAME.png

  • FOLDER_OUTPUT/plots/power_spectrum_NAME.png

Names for plots will not increment; in the event of repeated names, later plots will overwrite earlier ones.

Image Conversion Patterns

See also Convert Particles

Inputs

Cryo-EM images required, in mrcs or mrc formats. Microscope parameters depends on the wrapper function being used (either STAR or cs from cryoSPARC). Refer to the individual wrapper functions documentation.

In general, “indexed” wraqppers expect the metadata file to contain either a valid relative path to the MRC files, or expect the MRC file path basenames to govern (with the files themselves located in the directory pointed to by the folder_mrc parameter).

Outputs

Prefix set by the folder_output parameter.

Assume folder_output = OUT and COUNTER is a 6-digit 0-padded count of the total number of stacks converted so far. Then:

  • OUT/fft/particles_fourier_stack_COUNTER.pt for Fourier-space image stacks

  • OUT/fft/particles_fourier_stack_COUNTER.npz for image metadata (stored alongside the Fourier-space image stack)

  • OUT/plots/PLOT_NAME for plots, if requested, where PLOT_NAME matches the stack name or is power_spectrum_stack_COUNTER.png for power spectrum plot

Likelihood Patterns

See also Image-to-Structure Likelihood Computation

Inputs

For Templates: the actual paths will be listed in the template_file_list.npy file under the directory pointed to by the folder_templates parameter.

For Images: We expect to look at the Fourier-space image stacks stored following the output conventions of the image conversion process. Specifically, FP/fft/particles_fourier_stack_NUMBER.pt, where FP is the value of the folder_particles parameter and NUMBER is a 6-digit 0-padded increment.

Outputs

The exact files written will depend on the output type requested.

In general, if the folder_output parameter is set to OUT, all outputs will be under OUT/templateN, where N is the index number of the template in the templates list (i.e. the i_template parameter).

Then:

  • Cross-correlation outputs will go under OUT/templateN/cross_correlation/

  • Optimal-pose outputs will go under OUT/templateN/optimal_pose/

  • Integrated and log-likelihood outpus will go under OUT/templateN/log_likelihood/