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Reconstruction Parameters » History » Revision 10

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Amber Herold, 05/31/2011 12:57 PM


Reconstruction Parameters

Name a.k.a. Description Used By Required in interface? Notes
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
MRA - min radius for rotational alignment in pixels imagic
MRA - max radius for rotational alignment in pixels imagic
firstring Any pixels this far away from center will not be used spider
lastring Only pixels this far away will be used spider
xysearch translational search during projection matching will be limited to this many pixels from the center ofthe image spider
Symmetry Group sym ex. c1, c2... xmipp,eman,frealign,spider,imagic
Number of iterations iteration number xmipp
Mask Filename xmipp
Angular reconstitution angular increment of forward projections, ang inc of euler search, fraction of best ordered images to keep imagic
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
angular increments list of angular increments for projection mapping spider
MRA - angular increment of forward projections imagic
maxshift max translation during image alignment in pixels eman
xyshift particles only allowed to shift this far from center spider
MRA - max radial shift compared to original images imagic
MRA - max radial shift during this iteration imagic
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
Approximate mass in Kd imagic
MSA - percentage of images to ignore when calculating eiganimages imagic
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
keep determines which particles are kept for back-projection, -1 is one standard deviation worse than mean spider
MSA - fraction of final class averages to keep imagic
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
lp filtering low pass filter in angstroms spider, imagic
hp filtering high pass filter in angstroms spider, imagic
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
MSA - num class averges to produce from raw images imagic
MSA - num factors to use for classification imagic
MSA - percentage of worst class members to ignore after classification imagic
threed reconstruction object size, low-pass filter 3d volume imagic
Center stack prior to alignment imagic
Mirror references for alignment imagic

Updated by Amber Herold over 13 years ago · 10 revisions