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gpu_isac [2020/05/29 18:47] fschoenfeld |
gpu_isac [2020/08/03 13:48] fschoenfeld |
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===== Overview ===== | ===== Overview ===== | ||
+ | |||
+ | Bleuep! | ||
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+ | * .. | ||
+ | * .. | ||
+ | * .. | ||
+ | * .. | ||
+ | * .. | ||
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**ISAC** (Iterative Stable Alignment and Clustering) is a 2D classification algorithm to sort cryo-EM particles into classes depicting the same view of a target protein. It is based around iterations of | **ISAC** (Iterative Stable Alignment and Clustering) is a 2D classification algorithm to sort cryo-EM particles into classes depicting the same view of a target protein. It is based around iterations of | ||
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<note important> | <note important> | ||
- | **Beta | + | **Chimera |
</ | </ | ||
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- **Extract the archive** to your chosen GPU ISAC installation folder. | - **Extract the archive** to your chosen GPU ISAC installation folder. | ||
- **Open a terminal** and navigate to your installation folder. | - **Open a terminal** and navigate to your installation folder. | ||
- | - **Untar the archive** | + | - **Untar the archive**: < |
- **Check CUDA path variables** using: | - **Check CUDA path variables** using: | ||
- | - '' | + | - < |
- | - '' | + | - < |
- | - If the path variables do **not** contain these path variables, you can add them like so: | + | - If the path variables do **not** contain these path variables, you can add them like so: < |
- | * '' | + | export LD_LIBRARY_PATH=/ |
- | * '' | + | |
- | * Here '' | + | |
- **Compile the GPU ISAC C++/CUDA library:** | - **Compile the GPU ISAC C++/CUDA library:** | ||
- | - '' | + | - < |
- | - '' | + | - < |
- **Adjust sparx libraries** to work with the C++/CUDA library we just compiled: | - **Adjust sparx libraries** to work with the C++/CUDA library we just compiled: | ||
- | - '' | + | - < |
- | - '' | + | - < |
- | - '' | + | - < |
- **Set the correct libraries and environment: | - **Set the correct libraries and environment: | ||
- | - '' | + | - < |
- | - '' | + | - < |
- | - '' | + | - < |
- | - '' | + | - < |
+ | - **Bugfix for the Chimera beta:** | ||
+ | - < | ||
===== Usage ===== | ===== Usage ===== | ||
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* Replace '' | * Replace '' | ||
* Replace '' | * Replace '' | ||
- | * Adjust the number in '' | + | * Adjust the number in '' |
**[?] - Optional** parameters in the GPU ISAC call: | **[?] - Optional** parameters in the GPU ISAC call: | ||
* In '' | * In '' | ||
- | * Using '' | + | * Using '' |
* You can also use ''< | * You can also use ''< | ||
- | * Similarly, you can also use '' | + | * Similarly, you can also use '' |
< | < |