Sealy Center for Structural Biology/UTMB Workshop on CryoEM Data Processing

May 6-9 2019

Sessions will alternate between theory talks and tutorial sessions. Participants will need to use their own laptops to participate in the tutorials (see below).

The schedule does not include time for software installation. We will begin doing tutorials almost immediately. Make sure software is preinstalled and tested!

Lecture notes are archived at the bottom of the page. For your reference, not required for the practical sessions.

Laptop Requirements

What if my laptop doesn't meet these specifications?

YOU MUST INSTALL AND TEST SOFTWARE AND DATA BELOW IN ADVANCE IF YOU WISH TO PARTICIPATE!

Please install the software and insure it works before the workshop. If you have problems ask for help by email before the workshop!

Note that we're using several different software packages at the workshop, and you should install them all, but for days 1-3, installing EMAN2 will provide everything you need (since this installation also gets you SPHIRE). The other software will be used on the final day.

EMAN2/SPHIRE/SPARX

Software:

Data and Tutorials (please download and make sure you have working space on your computer):

SPHIRE (day 3)

UCSF Chimera

COOT (day 4)


PHENIX (day 4)

NAMD Flexible Fitting

Lecture Notes

These are for you reference and are not required for the tutorials. They will become available gradually during the workshop. Items showing in bright blue are not yet available.

#

Speaker

Topic

File

Mo1

Ludtke

Tomography and EMAN2 Intro

Mo1_Ludtke_Tomography.pdf

Mo2

Ludtke

High Resolution Subtomogram Averaging

Mo2_Ludtke_HighResTomo.pdf

Mo3

Chen

CryoET workflow

Mo3_Chen_cryoet.pdf

Mo4

Chen

Deep Learning in CryoEM/CryoET

Mo3_Chen_DeepLearning.pdf

Tu1

Ludtke

Single Particle Intro

Tu1_Ludtke_SPAIntro.pdf

Tu2

Sherman

CTF and Micrograph Quality

Tu2_Sherman_CTF.pdf

Tu3

Chen

Particle Picking

Tu3_Chen_Picking.pdf

Tu4

Shaikh

Initial Model Building Strategies

Tu4_Shaikh_InitialModel.pdf

We1

Ludtke

Quick software survey

We1_Ludtke_OtherSoftware.pdf

We2

Ludtke

Variability

We2_Ludtke_Variability.pdf

We3

Baker

Symmetry

We3_Baker_Symmetry.pdf

We4

Shaikh

Sphire

We4_Shaikh_Cryolo.pdf

We4

Shaikh

Sphire - Reproducibility

We4_Shaikh_Reproducibility.pdf

We5

Baker

Resolution

We5_Baker_Resolution.pdf

Th1

Ludtke

EMAN2 in Python

Th1_Ludtke_Python.pdf

Th2

Afonine

Phenix

Th2_Afonine_Phenix.pdf

Th3

Baker

Chimera

Th3_Baker_Chimera.pdf

Th4

Lynch

Flexible Fitting

Th4_Lynch_FlexibleFitting.pdf

Th5

Smith

Coot

Th5_Smith_Coot.pdf

Th6

Yen

Automation

Th6_Yen_Automation.pdf


If you have any general questions about things on this page, please email Steve Ludtke <sludtke@bcm.edu>

UTMBWorkshop2019 (last edited 2019-05-14 17:52:13 by SteveLudtke)