Cryo EM Map to Model Fitting & Real Space Refinement — Hands-on

Gain practical skills in cryo EM map to model pipelines, from understanding maps and resolution to fitting, refining and validating atomic models in real space. This module walks through inspection of cryo EM maps, initial rigid body and flexible fitting, iterative real space refinement, validation metrics and preparation of deposition ready structures and figures.

Cryo EM Map to Model Fitting & Real Space Refinement

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Session Index

Session 1 — Cryo EM Maps, Resolution & Features Session 2 — Initial Model Placement & Rigid Fitting Session 3 — Real Space Refinement & Flexible Fitting Session 4 — Validation, Deposition & Case Study

Session 1

Fee: Rs 8800

Cryo EM Maps, Resolution & Features

Cryo EM maps and resolution concepts

map formats and voxel size global and local resolution FSC curves and filtering ideas

Visual inspection and map preparation

contour levels and noise assessment sharpening and blurring strategies segmentation and masking overview

Recognising map features at different resolutions

secondary structure elements side chain visibility range ligand and cofactor densities

Session 2

Fee: Rs 11800

Initial Model Placement & Rigid Fitting

Starting models and homology inputs

choice of PDBs or predicted models sequence alignment and trimming domain and subunit segmentation

Rigid body fitting and docking into maps

manual docking workflows automatic fitting tools overview cross correlation based scores

Building a consistent assembly model

symmetry and biological assemblies interfaces and clashes check saving intermediate models safely

Session 3

Fee: Rs 14800

Real Space Refinement & Flexible Fitting

Local rebuilding and flexible fitting concepts

adjusting loops and side chains secondary structure restraints handling low resolution regions

Real space refinement workflows

geometry and stereochemistry checks map model correlation optimisation weighting and restraint strategies

Ligands, cofactors and waters in cryo EM maps

identifying convincing density parameterisation and restraints overview avoiding over interpretation of features

Session 4

Fee: Rs 18800

Validation, Deposition & Case Study

Map model validation metrics

global and local fit scores geometry and clash scores overfitting and cross validation ideas

PDB and EMDB deposition readiness

file organisation and naming metadata and annotation checklist common validation server outputs

End to end cryo EM map to model case study

from map inspection to refined model figures for manuscripts and talks documenting decisions and limitations

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Cryo EM Map to Model Fitting & Real Space Refinement Training | From Map to Deposition Ready Model

Cryo EM Map to Model Fitting & Real Space Refinement — Hands-on