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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 [[http://eman2.org/Install/BinaryInstallAnaconda/2.22|Installation Instructions]] before downloading
  * Please install [[https://cryoem.bcm.edu/cryoem/downloads/view_eman2_version/29|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):
  * Day 1
    * [[http://blake.bcm.edu/dl/tutorial_tomo_mini.zip|Tomography Small-tutorial Data Download]] (Day 1)
    * [[EMAN2:e2TomoSmall|EMAN2 tomography workflow tutorial (small)]]
  * Day 2/3
    * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Single Particle Reconstruction Data Download]] (Day 2)
    * [[http://blake.bcm.edu/dl/fassub.tgz|2-D Variability Data]] (Day 3)
    * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-3Tutorial.pdf]]

  * If you experience e2display.py crashing on the Mac, try this command to fix the problem : 
    * //conda install eman-deps=14.1=1 -c cryoem -c defaults -c conda-forge//
  * If you experience e2display.py crashing on Windows 10 using the Ubuntu method, with an error related to GLU, try:
    * sudo apt-get install libglu1-mesa libglu1-mesa-dev
  * If you have problems please email Steve Ludtke <sludtke@bcm.edu>

=== SPHIRE (day 3) ===
  * Installing EMAN2 above will get you the basic SPHIRE install, but for CRYOLO, you also need:
    * [[http://sphire.mpg.de/wiki/doku.php?id=downloads:cryolo_1&redirect=1]]
  * The SPHIRE demo will focus on looking at precomputed results, there is a full version (30 GB):
    * [[http://blake.grid.bcm.edu/dl/UTMB2019/precalculated_results_big.tar]]
    * or [[ftp://ftp.gwdg.de/pub/misc/sphire/SPHIRE_WORKSHOP_2019_05/precalculated_results_big.tar]]
  * And a reduced version missing some of the raw data (15 GB, download one or the other, not both):
    * [[http://blake.grid.bcm.edu/dl/UTMB2019/precalculated_results_small.tar]]
    * or [[ftp://ftp.gwdg.de/pub/misc/sphire/SPHIRE_WORKSHOP_2019_05/precalculated_results_small.tar]]

=== UCSF Chimera ===
  * Please install a recent version of [[https://www.cgl.ucsf.edu/chimera/download.html|UCSF Chimera]]
  * Difficulties in installing Chimera are unlikely, but please use the Chimera mailing list if you have issues.

=== COOT (day 4) ===
  * Please download this data to work with: [[http://blake.bcm.edu/dl/EMAN2/coot_demo_data.tgz]]
<<BR>>
  * [[https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/|Coot]] is a bit tricky to set up, and will only be used for one session on the final day. 
  * Linux is the primary supported platform.
  * Linux - [[https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/]]
  * Mac - [[https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/pre-releases/experimental/]]
  * Windows - [[http://bernhardcl.github.io/coot/wincoot-download.html]]
  * Please contact the developers directly for installation help

=== 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): 
    * [[http://phenix-online.org/download/nightly_builds.cgi]]
  * Phenix installation instructions are available here:
    * [[http://phenix-online.org/documentation/install-setup-run.html]]

  * 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 [[http://blake.bcm.edu/dl/EMAN2/namd_tutorial.zip|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 || [[http://blake.bcm.edu/dl/EMAN2/Mo1_Ludtke_Tomography.pdf]] ||
|| Mo2 || Ludtke || High Resolution Subtomogram Averaging || [[http://blake.bcm.edu/dl/EMAN2/Mo2_Ludtke_HighResTomo.pdf]] ||
|| Mo3 || Chen || CryoET workflow || [[http://blake.bcm.edu/dl/EMAN2/Mo3_Chen_cryoet.pdf]] ||
|| Mo4 || Chen || Deep Learning in CryoEM/CryoET || [[http://blake.bcm.edu/dl/EMAN2/Mo3_Chen_DeepLearning.pdf]] ||
|| Tu1 || Ludtke || Single Particle Intro || [[http://blake.bcm.edu/dl/EMAN2/Tu1_Ludtke_SPAIntro.pdf]] ||
|| Tu2 || Sherman || CTF and Micrograph Quality || [[http://blake.bcm.edu/dl/EMAN2/Tu2_Sherman_CTF.pdf]] ||
|| Tu3 || Chen || Particle Picking || [[http://blake.bcm.edu/dl/EMAN2/Tu3_Chen_Picking.pdf]]||
|| Tu4 || Shaikh || Initial Model Building Strategies || [[http://blake.bcm.edu/dl/EMAN2/Tu4_Shaikh_InitialModel.pdf]]||
|| We1 || Ludtke || Quick software survey || [[http://blake.bcm.edu/dl/EMAN2/We1_Ludtke_OtherSoftware.pdf]]||
|| We2 || Ludtke || Variability || [[http://blake.bcm.edu/dl/EMAN2/We2_Ludtke_Variability.pdf]]||
|| We3 || Baker || Symmetry ||[[http://blake.bcm.edu/dl/EMAN2/We3_Baker_Symmetry.pdf]] ||
|| We4 || Shaikh || Sphire ||[[http://blake.bcm.edu/dl/EMAN2/We4_Shaikh_Cryolo.pdf]] ||
|| We4 || Shaikh || Sphire - Reproducibility ||[[http://blake.bcm.edu/dl/EMAN2/We4_Shaikh_Reproducibility.pdf]] ||
|| We5 || Baker || Resolution ||[[http://blake.bcm.edu/dl/EMAN2/We5_Baker_Resolution.pdf]] ||
|| Th1 || Ludtke || EMAN2 in Python ||[[http://blake.bcm.edu/dl/EMAN2/Th1_Ludtke_Python.pdf]] ||
|| Th2 || Afonine || Phenix ||[[http://blake.bcm.edu/dl/EMAN2/Th2_Afonine_Phenix.pdf]] ||
|| Th3 || Baker || Chimera ||[[http://blake.bcm.edu/dl/EMAN2/Th3_Baker_Chimera.pdf]] ||
|| Th4 || Lynch || Flexible Fitting ||[[http://blake.bcm.edu/dl/EMAN2/Th4_Lynch_FlexibleFitting.pdf]] ||
|| Th5 || Smith || Coot ||[[http://blake.bcm.edu/dl/EMAN2/Th5_Smith_Coot.pdf]] ||
|| Th6 || Yen || Automation ||[[http://blake.bcm.edu/dl/EMAN2/Th6_Yen_Automation.pdf]] ||

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