From eeb641583707dfe54814e8e4da1064abbe64aba9 Mon Sep 17 00:00:00 2001 From: Michal Grzadkowski Date: Wed, 11 Sep 2024 10:13:42 -0400 Subject: [PATCH] updating README --- README.md | 15 ++++++++++----- cryodrgn/commands_utils/fsc.py | 1 + 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index aa909f8b..05d2e05b 100644 --- a/README.md +++ b/README.md @@ -299,12 +299,14 @@ Example usage: $ cryodrgn backproject_voxel projections.128.mrcs \ --poses pose.pkl \ --ctf ctf.pkl \ - -o backproject.128.mrc + -o backproject.128 \ + --first 10000 -The output structure `backproject.128.mrc` will not match the consensus reconstruction exactly -as the `backproject_voxel` command backprojects phase-flipped particles onto the voxel grid, -and by default only uses the first 10k images. -If the structure is too noisy, you can increase the number of images that are used with the `--first` argument. +The output structure `backproject.128/backproject.mrc` will not match the consensus reconstruction exactly +as the `backproject_voxel` command backprojects phase-flipped particles onto the voxel grid, and because here we +performed backprojection using only the first 10k images in the stack for quicker results. +If the structure is too noisy, we can try using more images with `--first` or the +entire stack instead (without `--first`). **Note:** If the volume does not resemble your structure, you may need to use the flag `--uninvert-data`. This flips the data sign (e.g. light-on-dark or dark-on-light), which may be needed depending on the @@ -581,6 +583,9 @@ These scripts are located in the `analysis_scripts` directory within the source [3] In particular, you may find it useful to perform filtering of particles separately from other analyses. This can done using our interactive interface available from the command line: `cryodrgn filter 01_cryodrgn256`. +[4] `--Apix` only needs to be given if it is not present (or not accurate) in the CTF file that was used in training. + + ### Generating additional volumes A simple way of generating additional volumes is to increase the number of k-means samples in `cryodrgn analyze` diff --git a/cryodrgn/commands_utils/fsc.py b/cryodrgn/commands_utils/fsc.py index 6ec8cd82..de11f088 100644 --- a/cryodrgn/commands_utils/fsc.py +++ b/cryodrgn/commands_utils/fsc.py @@ -337,6 +337,7 @@ def calculate_cryosparc_fscs( if out_file is not None: fsc_vals.reset_index(inplace=True, drop=False) logger.info(f"Saving FSC values to {out_file}") + fsc_vals.columns = fsc_vals.columns.str.replace(" ", "") fsc_vals.round(6).to_csv(out_file, sep=" ", header=True, index=False) return fsc_vals