CryoEM Club at UMass Chan

• Cryo-EM Club at UMass Chan
  • Upcoming Meetings
  • Past Meetings & Materials

FAQ

• FAQ
  • How do I …
  • What is …

Training Contents and Materials

• Cryo-EM Training - Basic (level I & II)
  • Level I - Basic TEM Operation (4 sessions)
  • Level II - Cryo TEM Operation (4 sessions)
• SerialEM Training - Basic, Tomography, Single Particle, Advanced
  • SerialEM - Basics (3 sessions)
  • SerialEM - Tomography (5 sessions)
  • SerialEM - Single Particle (5 sessions)
  • SerialEM - Advanced Topics (3 sessions)

Instructions, Manuals and Protocols

• CM120 Operation Instruction
  • Check log book to see if there have been any problems
  • Check vacuum status
  • Add Liquid Nitrogen to the BIG anti-contaminator dewar
  • Apply High Tension
  • Turn filament on
  • Check saturation and gun tilt, and then saturate the filament
  • Check C2 aperture mechanical position and C2 stigmatism
  • Check specimen holder & load grid
  • Insert specimen holder into column
  • Adjust the specimen height to the eucentric height
  • Check Beam Tilt Pivot Point X, Y
  • Check voltage and current rotation centers
  • Put in objective aperture and center it
  • Check Objective Lens stigmatism
  • Low-Dose Setup
    • Magnification setup for three modes
    • Align an identified area under Exposure and Search
  • Finishing Up
• CCD Cameras on CM120
  • Some Basic Properties of the Two Cameras
  • Shutter Control - Background Inforamtion
  • Shutter Control Setup for Orius 831 and TemCam 224HD
  • A Note about the Temperature
  • Control both cameras using SerialEM
  • Electron Dose
  • Pixlesize Calibration for Both Cameras
• Making Graphene Oxide Grid
  • Materials and Equipment Used:
  • Procedure:
• Single Particle Data Collection Using SerialEM
  • Check Scope Condition and Perform Tuning
  • Prepare Cameras
  • Make Low Mag Montage (LMM) Map or Grid Atlas
  • Setup Low Dose Condition
  • Make Medium Mag Montage Maps
  • Draw Grids Points for Each Mesh
  • Test Main Script to Run
  • Final Checking
  • Run it!
• Post Processing K2/K3 Frames from SerialEM Data Collection
  • For K2 camera on Talos Arctica
• Align Movie Frames with SerialEM and IMOD Programs
  • Alignframes
  • Framewatcher
  • Using GPU
  • On K2 Computer
  • Align using SerialEM directly
• Monitor Data Collection In The Fly
  • Setup for Shipping, alignframes and CTFfindPlot
  • End Results - CTF ploting and JPG of aligned image & power Spectrum
• Pixelsize and Distortion Info on K2/3 Cameras
  • On Talos Arctica
  • On Titan Krios
• Relion and cisTEM Docker Services
  • Relions
  • cisTEM
• cisTEM detaching and re-attaching sessions
  • Installing Xpra on Linux
  • Usage Examples
• Adding a Scalebar to Images
  • Overview
  • Prerequistes
  • Script Download
  • Editing the Script
  • Running the Script
• Setup Simple Lab Electronic Logbook
  • Elog
  • Config
  • Install on FreeBSD

SerialEM Notes

• SerialEM Note: Installation and Calibration
  • Installation
  • Calibration
• SerialEM Note: Two Scripts for High-Focus Calibrations
  • For High-Focus Mag
  • For High-Focus IS
• SerialEM Note: Make All LMM Maps Automatically
  • Procedure
  • Convert LMM maps into JPEG format
• SerialEM Note: Setup Dummy Instance
  • On the same computer
  • On a remote computer
  • Make Multiple Dummies For Different Scopes
  • On a Mac computer
• SerialEM Note: Setup LD with Mix of µP and nP Modes
  • Procedure Setting Up LD with µP and nP
• SerialEM Note: More About X,Y Positioning
  • The script lines
  • Explanations Line by Line
  • Just Using Stage Shift
  • Other thoughts
• SerialEM Note: More About Z Height
  • Background Information
  • Z_byV2 Function
  • Find the Offset Value using Script FindOffset
  • Note about Damping Factor
• SerialEM Note: Speed, Speed and Speed
  • Minimize Mag Switch
  • Order of Actions
  • Using Beam Tilt for Z Height Change
  • Relaxing Stage After Moving to Target
  • Using Compression on K2 Data
  • Using Local HDD or SSD
  • Using Multishot
• SerialEM Note: Tackle the Coma
  • Background
  • Linearity relationship between Image Shift and Induced Beam Tilt
  • Procedue to correct the coma induced by image-beam shift in SerialEM
• SerialEM Note: Utilize JPG File format
  • Save Map Overview to JPG
  • Save Single Shots to JPG
• SerialEM Note: Setup Email on K2 Computer
  • Setup SMTP and Relay Service
  • On SerialEM Part
• SerialEM Note: K3 is installed on Talos
  • Installation Went Smooth
  • SerialEM Control
  • Shutter Control
  • Other things to Watch
  • Additional Info
• SerialEM Note: Adding Point Items by Template Matching
  • Install
  • Usage
• SerialEM Note: Refine ZLP on Au Foil Grids
  • Background Information
  • Timer Function Commands
  • Use the Timer Functions
• SerialEM Note: Flexible Timer
  • Background information
  • Flexible Timer
• FastTomo: A Hybrid Approach to Speedup Tomography Data Collection
  • Some Brief background Information
  • FastTomo Script
  • A Few Points to Discuss
• SerialEM Note: Hidden Goodies
  • Example 1 - delete multiple nav items at once
  • Example 2 - make multiple polygon montage maps at once
  • Example 3 - make snapshot with nav features
  • Example 4 - Run script at SerialEM program start or exit
  • Example 5 - Scripting With Python
  • Example 6 - Centering Feature by Right Double Click
• SerialEM Note: Scriptless Control
  • Background Information
  • The New “Acquire at Items” Dialog Window
  • An Example Configuration for Single Particle
  • A Couple of Extra Notes
• SerialEM Note: Eucentricity With Beam Tilting
  • System Calibrations
  • Session Calibration
  • Eucentricity by Focus
• SerialEM Note: Define Image Shift Vectors for Multiple Exposure
  • The Manual Way
  • Using Hole Vectors
  • Adjustment Transform
  • A Smarter and More Automated Way
• SerialEM Note: Running A Script During Montaging
  • Enable it by a property
  • Case Studies
• SerialEM Note: Cross-mag Alignment
  • Set Image Shift Offset for LD View or Search Automatically
  • Realign a Feature in View map to Match Preview/Record
• SerialEM Note: Work With A Hex Grid
  • Finding Holes for Hex grid
  • Multiple Exposure Setup for Hex
  • Skipping a hole
  • Erase Periodic Peaks
• SerialEM Note: Adding Mesh Polygon by a Single Click
  • Autocontour
• SerialEM Note: Understanding Transformations in Multigrid Operation
  • Shift To Marker Transform
  • Realign Reloaded Grid Transform
  • Multishot in Multigrid
  • Hole Vectors Are Also Transformed Upon Reloading
• SerialEM Note: Debug Beam Instability
  • Background Information
  • Experiment
  • Plotting Results
• SerialEM Note: An Alternative Way to Center a Hole
  • Two Examples
  • To Center to the invisible hole in the middle of 4 holes
• SerialEM Note: An Alternative Way to Center a Mesh in LM
  • Center a Mesh
  • The Script
• SerialEM Note: More on MMM Centering
  • The Script to Run after Z change
• SerialEM Note: Early Adaption To UTAPI
  • In Property File
  • What If There Is A Problem
• SerialEM Note: Touch Up Low-Dose Offsets for IS and Defocus
  • To Fix IS Offset
  • To Fix Defocus Doubling Issue

Index

• Index