Helical Image Processing (PHOELIX)¶

General Workflow:¶

1. Make sure that the appropriate run name and directory tree are specified. Appion increments names automatically, but users are free to specify proprietary names and directories.
2. Enter the directory tree where the mandatory files are located. These files include llbo.sa, strong.sa, range.sa, cutfit1.dek, cutfit2.dek, cutfit3.dek, chop1.dek, chop2.dek, and template. If you do not have these files already, run preHIP as described in the next section and follow the guided protocol to generate them.
3. Enter a description of your run into the description box.
4. Select the stack to process from the drop down menu. Note that stacks can be identified in this menu by stack name, stack ID, and that the number of particles, pixel and box sizes are listed for each.
5. Make sure that "Commit to Database" box is checked. (For test runs in which you do not wish to store results in the database this box can be unchecked. This box is deactivated when running preHIP).
6. Enter the Filament Parameters or verify the default values.
   • Number of Filament Segments -
   • Repeat Length -
   • Diameter -
   • Inner Diameter -
7. Enter the Processing Parameters or verify the default values.
   • Filament Segment Length -
   • Box Height -
   • Pad Value -
   • Phase Residual Cutoff -
   • Filter Value -
   • Binning -
   • Contrast Change -
8. Click on "Run HIP" to submit your job to the cluster. Alternatively, click on "Just Show Command" to obtain a command that can be pasted into a UNIX shell.

Running PreHIP:¶

1. Click the "Run PreHIP" checkbox which will activate the indexing parameters below it and display a warning message.
2. Fill in the Indexing Parameters
   • N-fold -
   • Maximum Layer Line -
   • Maximum Bessel Order -
3. Select either the "Use rise and twist" or "Use layer line/bessel order" radio button which will activate the parameters below it.
   • Rise and Twist -
   • (1,0),(0,1) LLBO -
4. Click "Just Show Command" to generate the UNIX shell command.
5. Note that the "Commit to Database" box is deactivated. preHIP is used only for generating the mandatory files and therefore the preliminary results are not stored to the database.