How do I use Phoelix ?
Before you start:
- Make sure you have enough room, it takes approximately 3GB of disk
space for the average dataset.
- There is a tag at the very last line of phoelix_params, setting
auto_remove_files=1, will automatically remove files we feel
are extraneous at the end of each run.
- Suprim has a feature in which a non-zero number must be embedded within the
image.f file prefix.
Phoelix uses template matching to calculate cross-correlation points used
for filament straightening:
- The template can simply be a portion of your filament (probably one on repeat),
or it can be a projection of an average.
- Actomyosin has an arrow head direction, pointing left or right. To save
computing time we have incorporated the use of a left and right template.
Copy templates to working directory, both right and left
templates must have the same name and .l or .r as extensions
(ie. template.l and template.r). If your specimen does not
have a "direction" simply make template.l and template.r the same
template, or you can modify s_am so it dosen't ask this question.
- The template can have any name.
Retrieve parameters files:
- > s_setup am
This copies the master_params and phoelix_params files
to your directory. Check these parameters !!!
These parameters control the use of tilt/shift calculations,
step size, predicted location of diffraction spots, etc...
To begin running running PHOELIX interactively:
> s_am filename.f template
You will need to:
- Select snake box points and direction of template to use.
- Check the cross-correlation points, delete some if necessary I would not
recommend adding any new ones.
- Check the spline curve, this displays how your filament will be straightened.
- Check the zeroes of the ctf and corrent if necessary.
- Check the peak range for the tilt and range search, correct if necessary.
All displays are now in TCL/TK format, to use:
- click left mouse button to select point
- to delete a point, move cursor over cross and click right mouse button
- to scroll image, hold down middle mouse button and move image
- to close window go to menu and select quit or use ctrl-Q
it is not necessary to select save, the programs automatically
saves the points when quiting
When PHOELIX is finished it generates about thirty files, now you
can check some of the important files.
If you have any problems contact us at: phoelix@scripps.edu
contents © 2000
awl