Project-wide Parameters

Spire expects the configuration to include a special SPIDER document file, usually called params.ext. Numbers that apply to the entire project, e.g., pixel size, or electron energy, are collected in this doc file and may be used by many Procedure files.

When a new project is created, the parameter form is presented:

In the parameter form shown here, the pixel size and electron energy are required fields. The pixel size is used to automatically compute other parameters: the maximum spatial frequency, the window size, and the particle size. The electron energy is used to automatically compute lambda (electron wavelength). Some of these default values are specific to the ribosome. Check that automatically computed values are valid for your project!

The parameters shown here are specific to the Procedure files at the reconstruction with reference projections web page (see params.html), but you can edit the default parameters in the configuration file. Each parameter must be enclosed in a <parm> tag, with either
3 elements : key (int), value (float), text briefly describing the parameter
  or
4 elements : key, value, text, [a list of choices]
The element must be separated by spaces.

Three-element lists are presented as entries, with the descriptive text as the label (e.g., pixelsize). Four-element lists are presented as drop-down menus which allow the user to select from a limited number of choices (e.g., file format).

<Parameters>
   <parm>1   0    zip flag ['do not unzip', 'unzip'] </parm>
   <parm>2   0    file format ['SPIDER', 'HiScan', 'Perkin Elmer', 'ZIscanner']</parm>
   <parm>3   0    width (pixels)</parm>
   <parm>4   0    height (pixels)</parm>
   <parm>5   0    pixel size (A)</parm>
   <parm>6   0    electron energy (kV)</parm>
   <parm>7   2.0  spherical aberration (mm)</parm>
   <parm>8   0.0  source size (1/A)</parm>
   <parm>9   0.0  defocus spread (A)</parm>
   <parm>10  0.0  astigmatism (A)</parm>
   <parm>11  0    azimuth (degrees)</parm>
   <parm>12  0.1  amplitude contrast ratio (0..1)</parm>
   <parm>13  1000 Gaussian envelope halfwidth (1/A)</parm>
   <parm>14  0    lambda</parm>
   <parm>15  0    max. spatial frequency</parm>
   <parm>16  1    decimation factor</parm>
   <parm>17  0    window size (pixels)</parm>
   <parm>18  0    particle size (pixels)</parm>
   <parm>19  0    magnification</parm>
   <parm>20  0    scanning resolution (in microns:7,14,etc)</parm>
</Parameters>