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| '''UNDER CONSTRUCTION''' | '''''Note: based on some early testing results today, we will likely have to have a 2.01 bugfix release for EMAN2 & SPARX at the end of the week. While there are only a few minor issues, they will cause problems for some users at the workshop if they aren't fixed. We will post a note here when the 2.01 release has been posted.''''' |
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| EMAN2 will be used throughout the workshop for various purposes and is required to participate in the tutorial sessions. Please download the release 2.0 version of EMAN2 for your computer at: |
You MUST use a current version of EMAN2 for the workshop, not an older release. If you have an old version installed, please upgrade to 2.01 at the end of the week, and be sure to run 'e2bdb.py -c' under the old version BEFORE installing the new version ! EMAN2 will be used throughout the workshop for various purposes and is required to participate in the tutorial sessions. We have just put out the first official release version of EMAN2 (2.0). You can download and install this version from : |
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| ''Note:'' We will be doing extensive testing of the tutorials this week. If we discover any last minor bugs, we will release a 2.01 version later in the week, and make an announcement on this page, and on the above software/data list page. You may delay installation until later in the week if this concerns you, but please don't wait until the day before the workshop, or we may not have enough manpower to reply. |
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| The data is provided as either a .zip file or a compressed tar archive. Please download ONE of these files and unpack it into your workshop folder : * [[attachment:eman2_2011_demo_data.tgz]] * [[attachment:eman2_2011_demo_data.zip]] |
The data is provided as either a .zip file or a compressed tar archive. Please download ONE of these files and unpack it into your workshop folder. Note that this is only the demonstration data for single particle reconstruction. You also need to visit the other download pages. : * [[http://blake.grid.bcm.edu/dl/EMAN11/eman2_2011_demo_data.tgz|eman2_2011_demo_data.tgz]] * [[http://blake.grid.bcm.edu/dl/EMAN11/eman2_2011_demo_data.zip|eman2_2011_demo_data.zip]] |
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| 1. Run 'e2speedtest.py'. If it will not run properly, check the [[http://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstall|installation tips page]]. Something didn't work right. * If it runs properly it will give you a 'speedtest score'. This is a relative indicator of how long it will take to perform refinements on a single core (CPU) on your computer. You can roughly multiply this by the number of cores to get a proper relative estimate. A fast, current generation Intel processor gives a score of ~4400. With 12 cores on a machine (even more will be possible soon), this gives an aggregate score for a single fast workstation of ~50,000. The workstations we will use at the workshop are several years old, and have speedtest scores of ~2000, with 2 cores. A good laptop will give a score of ~3000-3500 and have 2 cores. 1. At the command prompt, cd into the workshop/eman2/test directory and type 'e2display.py', then click on each of the 3 files you see in the browser in turn. Each should display an image or volume. 1. ... |
1. Run 'e2speedtest.py'. * If it will not run properly, check the [[http://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstall|installation tips page]]. Something didn't work right. * If it runs properly it will give you a 'speedtest score'. This is a relative indicator of how long it will take to perform refinements on a single core (CPU) on your computer. You can roughly multiply this by the number of cores to get a proper relative estimate. A fast, current generation Intel processor gives a score of ~4400. With 12 cores on a machine (even more will be possible soon), this gives an aggregate score for a single fast workstation of ~50,000. The workstations we will use at the workshop are several years old, and have speedtest scores of ~2000, with 2 cores. A good laptop will give a score of ~3000-3500 and have 2 cores. 1. At the command prompt: * cd into the workshop/eman2/test directory and type 'e2display.py' * click on each of the 3 files you see in the browser in turn. Each should display an image or volume. |
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| If any of these tests fail, and the installation FAQ doesn't help, please contact gtang@bcm.edu so he can assist you. | If any of these tests fail, and the installation FAQ doesn't help, please contact sludtke@bcm.edu so he can assist you. ---- '''Results data downloads''' Since the refinements can take some time to run, we have made the __complete__ refinement results for each of the 3 specimens available for download. These results show what you ''should'' get if you follow the full reconstruction tutorial to completion. |
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| These downloads are multiple GB each, particularly the Ribosome. If many people try to download them during the workshop, the network will slow to a real crawl. |
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| The full tutorial for the workshop is also provided as a PDF document, so you can follow along at your own pace, or for reference after the workshop. * [[attachment:eman2_2011_tutorial.pdf]] |
* [[http://blake.grid.bcm.edu/dl/EMAN11/groel-done.tbz|groel-done.tbz]] (3.7 gb) GroEL refined to 8.4 A resolution + some demonstrations of resolution exaggeration due to masking and insufficient angular sampling. * [[http://blake.grid.bcm.edu/dl/EMAN11/mmcpn-done.tbz|mmcpn-done.tbz]] (1.4 gb) mm-cpn refined to ~8.4 A resolution * [[http://blake.grid.bcm.edu/dl/EMAN11/ribosome-done.tbz|ribosome-done.tbz]] (9.5 gb) Ribosome refined to ~11 A resolution with a few different sets of parameters for comparison. |
EMAN2
Multiple days
Note: based on some early testing results today, we will likely have to have a 2.01 bugfix release for EMAN2 & SPARX at the end of the week. While there are only a few minor issues, they will cause problems for some users at the workshop if they aren't fixed. We will post a note here when the 2.01 release has been posted.
You MUST use a current version of EMAN2 for the workshop, not an older release. If you have an old version installed, please upgrade to 2.01 at the end of the week, and be sure to run 'e2bdb.py -c' under the old version BEFORE installing the new version !
EMAN2 will be used throughout the workshop for various purposes and is required to participate in the tutorial sessions. We have just put out the first official release version of EMAN2 (2.0). You can download and install this version from :
http://ncmi.bcm.tmc.edu/ncmi/software/software_details?selected_software=counter_222
installation instructions are provided at the download site. Please make sure you download the correct version for your computer. There are a number of possibilities. If you have any difficulty figuring out which version to download, or installation difficulties, contact gtang@bcm.edu.
Note: We will be doing extensive testing of the tutorials this week. If we discover any last minor bugs, we will release a 2.01 version later in the week, and make an announcement on this page, and on the above software/data list page. You may delay installation until later in the week if this concerns you, but please don't wait until the day before the workshop, or we may not have enough manpower to reply.
Note for advanced users: we strongly suggest using one of our precompiled binaries rather than trying to compile from source, due to the number of dependencies, and limited support resources before the workshop. As all EMAN2 command-line programs are written in python, considerable customization is already possible, even when using the binary distributions. The only users who need to compile from source are those who wish to write new low-level algorithms in C++ or (for the moment) those who wish to experiment with CUDA support.
The data is provided as either a .zip file or a compressed tar archive. Please download ONE of these files and unpack it into your workshop folder. Note that this is only the demonstration data for single particle reconstruction. You also need to visit the other download pages. :
Once you have installed the software and data, you can test the installation by :
- Run 'e2speedtest.py'.
If it will not run properly, check the installation tips page. Something didn't work right.
- If it runs properly it will give you a 'speedtest score'. This is a relative indicator of how long it will take to perform refinements on a single core (CPU) on your computer. You can roughly multiply this by the number of cores to get a proper relative estimate. A fast, current generation Intel processor gives a score of ~4400. With 12 cores on a machine (even more will be possible soon), this gives an aggregate score for a single fast workstation of ~50,000. The workstations we will use at the workshop are several years old, and have speedtest scores of ~2000, with 2 cores. A good laptop will give a score of ~3000-3500 and have 2 cores.
- At the command prompt:
- cd into the workshop/eman2/test directory and type 'e2display.py'
- click on each of the 3 files you see in the browser in turn. Each should display an image or volume.
If any of these tests fail, and the installation FAQ doesn't help, please contact sludtke@bcm.edu so he can assist you.
Results data downloads Since the refinements can take some time to run, we have made the complete refinement results for each of the 3 specimens available for download. These results show what you should get if you follow the full reconstruction tutorial to completion.
These downloads are multiple GB each, particularly the Ribosome. If many people try to download them during the workshop, the network will slow to a real crawl.
groel-done.tbz (3.7 gb) GroEL refined to 8.4 A resolution + some demonstrations of resolution exaggeration due to masking and insufficient angular sampling.
mmcpn-done.tbz (1.4 gb) mm-cpn refined to ~8.4 A resolution
ribosome-done.tbz (9.5 gb) Ribosome refined to ~11 A resolution with a few different sets of parameters for comparison.