Parameter file for single particle reconstruction procedure files


This format is subject to change!!!

The document file is created by SPIRE or by the procedure file makeparams.spi. Most entries are entered interactively, while others (such as amplitude contrast) have "standard" values.

File format (2) and dimensions (3,4) refer to micrographs.

key name values or units
1 zip flag
0 : do not unzip
1 : needs to be unzipped
2 file format
0 : SPIDER
1 : HiScan tif
2 : Perkin Elmer
3 : ZI scanner
3 width (of micrograph, in pixels)
4 height (of micrograph, in pixels)
5 pixel size (in Angstroms)
6 electron energy (in keV)
7 spherical aberration (mm)
8 source size (1/A)
9 defocus spread (A)
10 astigmatism (A)
11 azimuth (degrees)
12 amplitude contrast ratio (0..1)
13 Gaussian envelope halfwidth (1/A)
14 lambda (A)
15 max. spatial frequency (1/A)
16 decimation factor (unitless positive number)
17 window size (pixels)
18 actual size (pixels)
19 magnification (unitless)
20 scanning resolution (7u, 14u, etc)

For example, a file created by makeparams.bat for micrographs that are not zipped, in tif format, with pixel size = 2.82 Angstroms, would look like the following:

 ;bat/dat   28-DEC-2000 AT 11:09:43   params.dat
    1 1  0.0000    
    2 1  1.0000    
    3 1  5336.0    
    4 1  6836.0    
    5 1  2.8200    
    6 1  200.00    
    7 1  2.0000    
    8 1  5.00000E-03
    9 1  0.0000    
   10 1  0.0000    
   11 1  0.0000    
   12 1  0.10000    
   13 1  10000.    
   14 1  0.025078    
   15 1  0.170648    
   16 1  2.0000    
   17 1  125.00    
   18 1  85.000    
   19 1  50000.000 
   20 1  7.000 

zip flag
Should be 1 if your micrographs have a *.gz extension.

file format
Refers to the file format of the raw micrograph.

width, height
Refer to the size of the raw micrograph. Used only for some formats where SPIDER cannot retrieve header information. These parameter values are ignored in SPIDER, ZI formats.

maximum spatial frequency
Computed as msf = 1/(2*pixelsize)
See also spatial frequency

decimation factor
Factor for reducing the size of the micrograph, using SPIDER's 'DC S' command. 2 = reduce to half size, 4 = reduce to 1/4 size, etc. It is often desirable to do an initial reconstruction with reduced size micrographs.

window size
Diameter (in pixels) of the small particle windows. This parameter is used by the particle picking procedure files, pick.spi and lfc_pick.spi. If the window size is set to zero, the procedure files will automatically compute it from the pixel size, using a standard size for the ribosome, window size = 368 Angstroms.

actual size (also called particle size)
Diameter (in pixels) of the particle. This value must be smaller than the window size. This parameter is used by the particle picking procedure files, pick.spi and lfc_pick.spi. If the actual size is set to zero, the procedure files will automatically compute it from the pixel size, using a standard size for the ribosome, actual size = 250 Angstroms.

magnification
Magnification factor of the electron microscope.

scanning resolution
Resolution used when digitizing film on the scanner.


Source: params.html     Updated: 2013/08/27     Tapu Shaikh