cryoem-halfmap-qc 0.5.1

Half-map QC and local reliability scores for cryo-EM density maps

cryoem-halfmap-qc

Local reliability scores and build zones for cryo-EM maps from half-maps and density features. Python 3.10+.

pip install cryoem-halfmap-qc
halfmap-qc          # interactive menu
halfmap-qc help     # CLI reference

Pipeline

Three commands, in order. Pass your own map paths and output directories.

# 1. Features from a map (.mrc / .map)
halfmap-qc features map.mrc --out features.npz --float32

# 2. Half-map metrics + correlations
halfmap-qc analyze \
  --features features.npz \
  --half1 half1.map --half2 half2.map \
  --reference ref.map \
  --contour CONTOUR \
  --out-dir analysis_out

# 3. Reliability score + build-zone MRCs
halfmap-qc reliability \
  --reference ref.map --half1 half1.map --half2 half2.map \
  --features features.npz \
  --halfmap-npz analysis_out/halfmap_metrics.npz \
  --contour CONTOUR \
  --out-dir reliability_out

--contour is the density threshold for the analysis mask (same value in steps 2 and 3). Optional: --local-res path.mrc on reliability for a local-resolution comparison figure.

Outputs: reliability_score and omit / caution / build zones as MRC overlays on your reference grid, plus .npz and summary JSON under --out-dir.

Flag details: halfmap-qc features --help, halfmap-qc analyze --help, halfmap-qc reliability --help.

HPC (ARC)

Default login python3 is too old (3.6). Conda modules load on compute nodes only:

srun -p compute1 -n 1 -t 02:00:00 --pty bash
module load miniconda/24.4.0
conda activate halfmap-qc    # after one-time: conda create -n halfmap-qc python=3.12 -y && pip install cryoem-halfmap-qc

Batch job — copy scripts/halfmap_qc_cluster.sbatch.example, set MAP, HALF1, HALF2, REF, CONTOUR, and submit. Each step aborts if the previous one fails.

cp scripts/halfmap_qc_cluster.sbatch.example run_my_map.sbatch
# edit paths in run_my_map.sbatch
sbatch run_my_map.sbatch

If install fails with empty (from versions:), check python --version (need ≥3.10) and pip install -U pip.

Citation

@software{mohanty2026cryoem_halfmap_qc,
  author = {Mohanty, Sarthak},
  title = {cryoem-halfmap-qc: local map reliability from cryo-EM density and half-maps},
  year = {2026},
  doi = {10.5281/zenodo.20618526},
  url = {https://doi.org/10.5281/zenodo.20618526},
  version = {0.5.0}
}

MIT — see LICENSE.