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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).

  • Day 1 - Tomography/Subtomogram Averaging (EMAN2.3 tutorial)
  • Day 2 - Single Particle Reconstruction (EMAN2.3 tutorial)
  • Day 3 - Single Particle Reconstruction (SPHIRE tutorial)
  • Day 4 - Model Building (Chimera/Coot/PHENIX)

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

  • Participants in the tutorial sessions will need to use their own laptop computers. While the tutorials are scaled back versions of 'real' problems, a reasonably powerful laptop computer is still required.
  • Recommended laptop specifications:
    • 4 cores, 2.0+ ghz processor (4 cores, not threads)
    • 16 GB RAM
    • 50 - 75 GB of free disk space
    • high resolution capable display (1080P or similar recommended)
    • Mac/Linux preferred.
      • SPARX/SPHIRE does not officially support Windows. If you use the Win10 embedded Ubuntu strategy for installing EMAN2/SPHIRE, it MAY be possible to make this work, but it is an unsupported configuration for SPHIRE.
      • The other software at the workshop (EMAN2, Chimera, PHENIX) does support windows, but:
        • Windows users will need to be familiar with working from the command-line (often windows users don't even realize it exists)
        • there can be many different machine-specific problems with installation under Windows. Users are very strongly encouraged to install and thoroughly test the installation ASAP.

What if my laptop doesn't meet these specifications?

  • With 2 cores jobs will run slower, so you may get a bit behind in the demos, but can probably still participate
  • Most tutorials will probably be ok with 8 GB of RAM, but you may have some interactivity problems, and it is possible a few very memory intensive tasks may not work right
  • While you will not need 75 GB of storage for any single day's demos, if you have less space than this you may, for example, have to move the first day's tutorial files to an external drive to make space for day 2 and so on...
  • If you really do not have a suitable laptop and are desperate, please contact mbsherma@UTMB.EDU who may be able to find a solution for a limited number of participants.

  • Due to the large number of participants (~100), is not a good idea to rely on any sort of remote desktop sharing to your home institution. It is very likely that it may not work (network congestion), or may work but have inadequate performance. If you decide to rely on this and it fails, we will not be able to help.

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:

  • Please read Installation Instructions before downloading

  • Please install EMAN2.3 (or a post 2.3 continuous build)

  • It is critical that you have EMAN2.3 or newer installed. EMAN2.22 lacks many newly developed features we will cover.
  • EMAN2 installation includes SPHIRE (and vice versa)

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

SPHIRE (day 3)

UCSF Chimera

  • Please install a recent version of UCSF Chimera

  • Difficulties in installing Chimera are unlikely, but please use the Chimera mailing list if you have issues.

COOT (day 4)


PHENIX (day 4)

  • Active participants are expected to bring their own laptop computers with Phenix and Coot installed.
  • Please download and install the latest stable release of PHENIX (1.15.2-3472):
  • Phenix installation instructions are available here:
  • To verify that Phenix and Coot are properly installed and functional:
    • Start Phenix GUI by typing phenix in the command line prompt or by clicking an executable icon;
    • Click on Coot icon located in the upper part of the GUI: this should start Coot;
    • If Coot starts -- check is complete. Close down Coot and Phenix.
  • For questions or download/installation issues please use help@phenix-online.orgwith "Galveston workshop" in the subject line.

NAMD Flexible Fitting

  • Wasn't actually done during the workshop, but tutorial files are available here

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)