# UCSF ChimeraX - II - Overview EM

### April 26, 2018

## Warning: package 'knitr' was built under R version 3.5.2

# Workshop goal

In this second section we’ll explore briefly electron density maps. This is usefulf for CryoEM data but also X-ray crystallography.

## Learning objectives

• Open a density map
• display density
• color etc.
• Close and quit

## NOTES on format

Embedded movies only appear within the HTML version of this document. For PDF and DOCX version refer to the foot notes for URL.

Note: If you are left-handed inverting Left and Right assignments might work better for you.

Note:

This button will invite you to act on suggested actions as we go along the workshop.

# Introduction

Some of the material presented here is inspired by a demonstration of ChimeraX by Tom Goddard (Programmer/Analyst, UCSF Resource for Biocomputing, Visualization, and Informatics) who develops the software. YouTube “Movie Making for cryoEM using ChimeraX.”1 (The movie is 49 min long.)

(Credit: SBGrid Consortium. Published on Apr 20, 2017)

## Background

The “Guide to Unterstanding PDB data2 provides important information on the methods used for the determination of atomic structures, biological assemblies, resolution, etc.

# Density maps

In previous workshops we have only worked with atomic coordinates. Density maps are the primary result of experimental analysis of CryoEM and X-Ray crystallography that scientists use to build atomic coordinates if the resolution is adequate. (For a comparison between CryoEM and X-Ray crystallography density maps see e.g. Wlodawer, Li, and Dauter (2017).)

A definition of resolution, in structure determinations, is the distance corresponding to the smallest observable feature: if two objects are closer than this distance, they appear as one combined blob rather than two separate objects3 (see also embedded movie4.)

(Credit: movie by James Holton[^CX23]) [^CX23]:http://bl831.als.lbl.gov/~jamesh/movies/

## What is a density map?

Electron density maps are obtained:

• in X-Ray crystallography: by diffraction
• in cryoelectron microscopy: by averaging 2D images in different orientations

In both cases complex mathematical formulae are used via computer software (including Fast Fourrier Transforms.) The final result is a series of grid points in space assigned with an electron density value: this is where matter is located.

### Cryo EM Maps

The video “A 3 minute introduction to CryoEM5 provides a good visual summary of the process:

(Credit: Gabe Lander Thesis defense, 2009. Published on Aug 17, 2011)

## X-Ray maps

The video “What is Cryo-Electron Microscopy (Cryo-EM)6 highlights both methods. The X-Ray method is summarized in 20 seconds (starting at 20 seconds in the movie and ending at 40 seconds.)

(Credit: GUC San Francisco (UCSF) - Published on May 28, 2015)

## Density map databases

Density maps may be deposited at The Electron Microscopy Data Bank (EMDB) that contain the same data but with different user interface or web functionality:

### Search PDB and EMDB

Structural entries may be combined with PDB entries from which there exists an atomic structure: http://emdatabank.org/search.html

Browse/search:

Resources:

#### Search PDB

Browse PDB entries determined using 3DEM methods:

# Exercise in ChimeraX

Help > Quick Start Guide

This will open a page within the internal web browser of ChimeraX. The page is LOCAL on your computer and part of the software installation.

SCROLL DOWN to the portion titled: “Example Density-Map Commands”

On THIS PAGE the commands are clickable and will be immediately applied within ChimeraX.

Note: it is also possible to open a version on the web (ChimeraX Quick Start Guide)11, however the commands are not click-and-execute as in the local verison.

You can then click on the pre-written commands and see the results within the graphical window.

# REFERENCES

Wlodawer, A., M. Li, and Z. Dauter. 2017. “High-Resolution Cryo-EM Maps and Models: A Crystallographer’s Perspective.” Structure 25 (10): 1589–97. https://doi.org/10.1016/j.str.2017.07.012.