Cryo-EM Data Interpretation & Structural Proteomics — Hands-on

Go from cryo EM map to defensible biological insight. Learn best practices for map inspection, sharpening/denoising, segmentation, model fitting/refinement, and validation—then enrich models with structural proteomics evidence such as crosslinking-MS, HDX, and native-MS to build coherent mechanistic stories.

Cryo-EM Data Interpretation & Structural Proteomics

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Session Index

Session 1 — Map Inspection, Resolution & Sharpening Session 2 — Segmentation, Fitting & Model Building Session 3 — Validation: EM Metrics & Refinement Session 4 — Mini Capstone: Proteomics Guided Interpretation

Session 1

Fee: Rs 6300

Map Inspection, Resolution & Sharpening

Global vs local resolution; anisotropy & masking effects

Theory

Map conditioning and visualization practices

local sharpen/denoise B-factor tuning ChimeraX/pyem

Quality flags before model fitting

map connectivity noise & overfitting cues

Session 2

Fee: Rs 8400

Segmentation, Fitting & Model Building

Map segmentation & subunit identification

ChimeraX/Segger watershed/thresholding

Rigid-body fitting & flexible refinement

Phenix dock in map ISOLDE/Coot edits AlphaFold prefit

Troubleshooting: heterogeneity, missing loops & symmetry

local rebuilds symmetry constraints

Session 3

Fee: Rs 11200

Validation: EM Metrics & Refinement

EM specific validation metrics & geometry checks

EMRinger Q-score FSC / map model CC MolProbity

Refinement workflows

Phenix real space refine PDB REDO concepts

Finalizing depositor ready bundles

figures/tables validation summaries

Session 4

Fee: Rs 14000

Mini Capstone: Proteomics Guided Interpretation

Integrate XL-MS/HDX/native-MS with the cryo EM model to support interfaces & dynamics

Theory + Practical

Evidence trails & provenance: from raw spectra to mapped restraints

distance filters coverage plots report bundle

Deliverables: figures, tables, README & manifest

PDF CSV/TSV checksums

PDF

Cryo-EM Data Interpretation & Structural Proteomics Training | Map → Model → Validate, +XL-MS/HDX Integration

Cryo-EM Data Interpretation & Structural Proteomics — Hands-on