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howto:sphire_helical [2019/09/29 14:59] mstabrin |
howto:sphire_helical [2019/10/01 12:38] twagner |
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Before you start the processing helical data, you have to switch to the Helical version of SPHIRE. | Before you start the processing helical data, you have to switch to the Helical version of SPHIRE. | ||
- | You can do that in the general settings area. | + | You can do that in the general settings area or start the GUI with **sphire %%--%%helical**. |
< | < | ||
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{{ : | {{ : | ||
- | Follow the steps of the normal SPA Tutorial for the steps up to the 3D refinement. | + | <note important> |
+ | Follow the steps of the normal | ||
+ | The information about the filament width should be filled out by default for these steps. | ||
+ | </ | ||
< | < | ||
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</ | </ | ||
- | {{ :howto:sphire_helical_meridien.png?600 |}} | + | {{ :howto:helical_refinement_unfilled.png?600 |}} |
+ | |||
+ | Fill out the information like in the **SPA** tutorial. | ||
+ | |||
+ | A short description for the additional options: | ||
+ | * **Theta min [degree]** - Minimum Theta to use during the EXHAUSTIVE step. (This should be kept to 90 for filamentous samples) | ||
+ | * **Theta max [degree]** - Maximum Theta to use during the EXHAUSTIVE step. (This should be kept to 90 for filamentous samples) | ||
+ | * **Group name for chunks** - The random chunks are created based on this header entry name. | ||
+ | * **Outlier group ID** - Outlier calculation is performed after every iteration. For now, they are only calculated, but not applied automatically. | ||
+ | * **Helical rise [A]** - Approximate helical rise of the protein. This information is used to limit the x/y-shift range in every iteration during the refinement. | ||
+ | |||
+ | A more detailed tutorial combined with a test dataset will follow soon. | ||
+ | |||
+ | If you encounter any problems or in case you have questions about the procedure feel free to ask in the [[howto: |