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Amber Herold, 05/31/2011 12:16 PM
Reconstruction Parameters¶
Name | a.k.a. | Description | Used By | Required in interface? |
---|---|---|---|---|
Mask Radius | mask | raduius of external map in pixels | xmipp, eman, imagic | |
Inner Radius | inner radius for alignment in pixels | xmipp | ||
imask | Particle inner mask radius | radius of internal mask (in pixels for eman and spider, Angstroms for frealign) | EMAN, frealign, spider | |
Outer Radius | xmipp | |||
Particle outer mask radius (RO) | mask | radius from center of particle to outer edge (frealign in angstroms, spider in pixels) | frealign, spider | |
amask | amask=[r],[threshold],[iter] | eman | ||
Symmetry Group | sym | ex. c1, c2... | xmipp,eman,frealign,spider,imagic | |
Number of iterations | iteration number | xmipp | ||
Mask Filename | xmipp | |||
Angular Sampling Rate | xmipp | |||
Max angular change | xmipp | |||
max change offset | xmipp | |||
Search range for 5d transitional search | xmipp | |||
Discard % of image with CCF below | xmipp | |||
Reconstruction Method | xmipp | |||
Values of lambda for ART | xmipp | |||
Initial max frequency used by reconstruct fourier | xmipp | |||
Compute resolution? | xmipp | |||
Low Pass Filter the reference? | xmipp | |||
Do not use estimated resolution for low-pass filtering? | xmipp | |||
Constant to add to the estimated resolution | xmipp | |||
ang | angular step for projections in degrees | EMAN | ||
maxshift | max translation during image alignment in pixels | eman | ||
hard | hard limit for make3d program | eman | ||
clskeep | =[std dev multipier] how many raw particles discarded for each class average | eman | ||
clsiter | iterative alignmnet to each other | eman | ||
filt3d | applies gaussian low pass filter in pixels [rad] | eman | ||
xfiles | =[mas in kD] | eman | ||
shrink | scale down by a factor of [n] before classification | eman | ||
euler2 | =[oversample factor] | eman | ||
median | use median value instead of average for each pixel | eman | ||
phscls | use signal to noise ratio weighted phase residual | eman | ||
refine | do subpixel alignment | eman | ||
tree | decimate reference populatiuon | eman | ||
coran | use coran algorithm | eman | ||
eotest | use even odd test | eman | ||
amplitude contrast (WGH) | frealign | |||
Standard deviation filtering | fealign | |||
Phase B-factor weighting constant (PBC) | frealign | |||
B-factor offset (BOFF) | frealign | |||
Number of randomized search trials (ITMAX) | frealign | |||
Number of potential matches to refine (IPMAX) | frealign | |||
Target phase residual (TARGET) | frealign | |||
Worst phase residual for inclusion (THRESH) | frealign | |||
Resolution limit of reconstruction (RREC) (in Ångstroms; default Nyquist) | frealign | |||
Lower resolution limit or high-pass filter (RMAX1) (in Ångstroms) | frealign | |||
Higher resolution limit or low-pass filter (RMAX2) (in Ångstroms; default 2*Nyquist) | frealign | |||
B-factor correction (RBFACT) (0 = off) | frealign | |||
Only use CTFFIND values | frealign | |||
Last particle to use | frealign | |||
firstring | Any pixels this far away from center will not be used | spider | ||
lastring | Only pixels this far away will be used | spider | ||
xysearch | spider | |||
lp | filtering | low pass filter in angstroms | spider, imagic | |
hp | filtering | high pass filter in angstroms | spider, imagic | |
xyshift | particles only allowed to shift this far from center | spider | ||
keep | determines which particles are kept for back-projection, -1 is one standard deviation worse than mean | spider | ||
angular increments | list of angular increments for projection mapping | spider | ||
MRA | multi-reference alignment of raw particles params | imagic | ||
MSA | multi-variate statistical analysis params | imagic | ||
Angular reconstitution | angular increment of forward projections, ang inc of euler search, fraction of best ordered images to keep | imagic | ||
threed reconstruction | object size, low-pass filter 3d volume | imagic | ||
Approximate mass in Kd | imagic | |||
Center stack prior to alignment | imagic | |||
Mirror references for alignment | imagic |
Updated by Amber Herold over 13 years ago · 5 revisions