This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
howto:sphire_helical [2019/09/27 17:38] twagner |
howto:sphire_helical [2019/10/01 12:38] twagner |
||
---|---|---|---|
Line 1: | Line 1: | ||
====== How to use SPHIRE Helical ====== | ====== How to use SPHIRE Helical ====== | ||
+ | |||
+ | < | ||
+ | This is the very first HowTo for filamentous reconstruction. | ||
+ | Note that we do not impose or require any information about the helical symmetry of your data. | ||
+ | |||
+ | --- | ||
+ | |||
+ | Another more detailed Tutorial including a filamentous test dataset will follow soon. | ||
+ | </ | ||
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**. |
< | < | ||
Line 15: | Line 24: | ||
You will notice that the logo in the lower left corner changes: | You will notice that the logo in the lower left corner changes: | ||
- | {{ :howto:sphire_helical.png?600 |}} | + | {{ :howto:sphire_helical_arrow.png?600 |}} |
+ | |||
+ | Fill out the information you have about your Protein: | ||
+ | |||
+ | {{ : | ||
+ | |||
+ | <note important> | ||
+ | Follow the steps of the normal [[downloads: | ||
+ | The information about the filament width should be filled out by default for these steps. | ||
+ | < | ||
+ | |||
+ | < | ||
+ | <div style=" | ||
+ | < | ||
+ | </ | ||
+ | </ | ||
+ | |||
+ | {{ : | ||
+ | |||
+ | 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. | ||
- | {{ :howto:sphire_helical_meridien.png? | + | If you encounter any problems or in case you have questions about the procedure feel free to ask in the [[howto:mailinglist|SPHIRE mailing list]] or write me directly: markus.stabrin@mpi-dortmund.mpg.de |