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--- howto:sphire_helical [2019/09/27 17:22]
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+++ howto:sphire_helical [2019/10/01 12:42]
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 ====== How to use SPHIRE Helical ======
-Before you start the processing helical data, you have to switch to the Helical version of SPHIRE. Your do that in the general settings area.
+<note>
+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.
+</note>
+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 or start the GUI with **sphire %%--%%helical**.
+<html>
+<div style="background-color: #cfc ; padding: 10px; border: 1px solid green;">
+<b>&#9658; Please press the [Switch to helical GUI] button</b>
+</div>
+</html>
 {{ :howto:sphire_normal.png?600 |}}
-{{ :howto:sphire_helical.png?600 |}}
+You will notice that the logo in the lower left corner changes:
+{{ :howto:sphire_helical_arrow.png?600 |}}
+Fill out the information you have about your Protein:
+{{ :howto:helical_project_filled.png?600 |}}
+<note important>
+**Follow the in-depth tutorial**
+Follow the steps of the normal [[downloads:sphire_1_3#tutorial|SPA Tutorial]] for the steps **up to** the 3D refinement.
+The information about the filament width should be filled out by default for these steps.
+</note>
+When you reached the step for 3D refinement:
+<html>
+<div style="background-color: #cfc ; padding: 10px; border: 1px solid green;">
+<b>&#9658; Please press the [3D Refinement (Alpha)] button</b>
+</div>
+</html>
+{{ :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.
-{{ :howto:sphire_helical_meridien.png?600 |}}
+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

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