---
# System prepended metadata

title: Treating cryo-EM data

---

% Density guided simulations
% Christian Blau
% 2019-12-09 - Janssen

# Treating cryo-EM data
  
## {data-background-image="pictures/emChallenges.svg" data-background-size="70%"}

# Fitting structures to densities

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![](pictures/old/input_density.png)

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![](pictures/old/input_structure.png)

##

![](pictures/old/input_density_structure1.png)

## {data-background-video="movies/fitanimation.mp4" data-background-size="80%"}

## Simulation setup requirements

 - "vanilla" GROMACS simulation
 - add density in .mdp options
 - apply forces that increase similarity with density

## Exploring structural ensembles

## {data-background-video="movies/fitanimation_md.mp4" data-background-size="80%"}

## {data-background-video="movies/forced_fit.mp4" data-background-size="80%"}

## Choice of force-constant

 - determine balance between influence from force-field and from map

## {data-background-video="movies/fitanimation_md.mp4" data-background-size="80%"}

## {data-background-video="movies/forced_fit.mp4" data-background-size="80%"}


# GLIC - avoiding model building

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![](pictures/glic.png)

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![](pictures/glic1.png)

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![](pictures/glic2.png)

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![](pictures/glic3.png)

# Connecting structure and density

## {data-background-image="pictures/scattering.svg" data-background-size="80%"}

## {data-background-image="pictures/scattering-transp.svg" data-background-size="80%"}

- EM densities report the number of electron-atom interactions per Volume

## Assumptions {#nobg}

![](pictures/old/scattering_2.svg)

- Interaction is defined by interaction cross-section and motion of atoms

## {data-background-image="pictures/model.svg" data-background-size="80%"}

## {data-background-image="pictures/model1.svg" data-background-size="80%"}

## {data-background-image="pictures/model2.svg" data-background-size="80%"}

## {data-background-image="pictures/model3.svg" data-background-size="80%"}

## {data-background-image="pictures/Prob_gaus.svg" data-background-size="80%"}

## {data-background-image="pictures/Prob_poisx.svg" data-background-size="80%"}

# Summary

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![](pictures/densfit1.png)

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![](pictures/densfit2.png)

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![](pictures/densfit3.png)

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![](pictures/template.png)
