Appion

Reconstruction Parameters » History » Revision 10

Revision 9 (Amber Herold, 05/31/2011 12:54 PM) → Revision 10/37 (Amber Herold, 05/31/2011 12:57 PM)

h1. Reconstruction Parameters 


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