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| === Written Tutorials we Will Use === * [[attachment:EMAN2-3Tutorial.pdf||&do=get]] * [[EMAN2/e2TomoSmall|EMAN2 tomography workflow tutorial (small)]] |
=== YOU MUST INSTALL AND TEST SOFTWARE AND DATA BELOW IN ADVANCE IF YOU WISH TO PARTICIPATE! === With a workshop with up to 100 participants it simply isn't possible to help a significant fraction of people on-site with software problems. Please install the software and insure it works before the workshop. If you have problems ask for help by email before the workshop! |
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| ==== 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) * EMAN2 installation includes SPHIRE (and vice versa) |
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| 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 * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Single Particle Reconstruction Data Download]] (Day 2) * [[attachment:EMAN2-3Tutorial.pdf||&do=get]] |
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| === Required Pre-workshop Software and Data === = Please do not install software/data now. Wait until after April 25th = ==== EMAN2/SPHIRE/SPARX ==== * We will be using EMAN2.3 (SPHIRE from the same release), which will be released by the 25th (assuming all goes well) * You MUST download/install/test all data/software before the workshop if you wish to participate. * If you have problems you must ask for help in advance. * There will be up to 100 participants, and no time is scheduled for software installation, so if the software doesn't work before you arrive, you will spend a lot of time just watching. We will not have the resources to help people with installation problems on-site. * Final information will be posted here By April 25th * [[http://blake.bcm.edu/dl/tutorial_tomo_mini.zip|Tomography Mini-tutorial Data Download]] |
* If you have problems please email Steve Ludtke <sludtke@bcm.edu> |
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| * Difficulties in installing Chimera are unlikely, but please use the Chimera mailing list if you have issues. ==== PHENIX ==== |
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| [[https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/|Coot]] is a bit tricky, and will only be used for one session on the final day. Linux is their primary supported platform. Please contact the developers directly for installation help! : | * [[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. |
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| * Please contact the developers directly for installation help | |
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| If you have any questions about things on this page, please email Steve Ludtke <sludtke@bcm.edu> | If you have any general questions about things on this page, please email Steve Ludtke <sludtke@bcm.edu> |
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)
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 at least 2 weeks in advance of the workshop.
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...
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!
With a workshop with up to 100 participants it simply isn't possible to help a significant fraction of people on-site with software problems. Please install the software and insure it works before the workshop. If you have problems ask for help by email before the workshop!
EMAN2/SPHIRE/SPARX
Software:
Please read Installation Instructions before downloading
Please install EMAN2.3 (or a post 2.3 continuous build)
- EMAN2 installation includes SPHIRE (and vice versa)
Data and Tutorials (please download and make sure you have working space on your computer):
- Day 1
- Day 2
If you have problems please email Steve Ludtke <sludtke@bcm.edu>
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.
PHENIX
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
If you have any general questions about things on this page, please email Steve Ludtke <sludtke@bcm.edu>