Reconstruction Parameters » History » Revision 26
Revision 25 (Amber Herold, 05/31/2011 02:58 PM) → Revision 26/37 (Amber Herold, 05/31/2011 02:58 PM)
h1. Reconstruction Parameters
|_.Name|_.a.k.a.|_.Description|_.Used By|_.Make common to all?|_.Notes|
|Outer Mask Radius|Particle outer mask radius (RO),Outer Radius, mask|radius from center of particle to outer edge (frealign in angstroms, spider in pixels), raduius of external map in pixels|frealign, spider,xmipp, eman, imagic|y||
|Inner Mask Radius|Inner Radius,Particle inner mask radius|inner radius for alignment in pixels|xmipp, frealign, spider|y|not xmipp|
|Outer Alignment Radius|||xmipp, eman, imagic|y|not eman, frealign|
|Inner Alignment Radius|||xmipp, eman, imagic|y|not eman, frealign|
|Symmetry Group|sym|ex. c1, c2...|xmipp,eman,frealign,spider,imagic|y||
|Number of iterations|iteration number||xmipp|y||
|Angular Sampling Rate|ang|angular step for projections in degrees|xmipp,EMAN|y|not frealign|
|Percentage of worst images to discard|||xmipp|y|not frealign|
|||||||
|imask||radius of internal mask (in pixels for eman and spider, Angstroms for frealign)|EMAN|||
||mask|||||
|amask||amask=[r],[threshold],[iter]|eman|||
|Mask Filename|||xmipp|||
|Max angular change|||xmipp|||
|max change offset|||xmipp|||
|Search range for 5d transitional search|||xmipp|||
|Reconstruction Method|||xmipp|||
|Values of lambda for ART|||xmipp|||
|Initial max frequency used by reconstruct fourier|||xmipp|||
|Compute resolution?|||xmipp||don't need this, should always be set to yes|
|filt3d||applies gaussian low pass filter in pixels [rad]|eman|||
|Low Pass Filter the reference?|||xmipp|||
|Do not use estimated resolution for low-pass filtering?|||xmipp|||
|Constant to add to the estimated resolution|||xmipp|||
|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|||
|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|||
|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|||
|MRA - min radius for rotational alignment in pixels|||imagic|||
|MRA - max radius for rotational alignment in pixels|||imagic|||
|MSA - fraction of final class averages to keep|||imagic|||
|MRA - angular increment of forward projections|||imagic|||
|MRA - max radial shift compared to original images|||imagic|||
|MRA - max radial shift during this iteration|||imagic|||
|MSA - percentage of images to ignore when calculating eiganimages|||imagic|||
|Angular reconstitution||angular increment of forward projections, ang inc of euler search, fraction of best ordered images to keep|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|||
|angular increments||list of angular increments for projection mapping|spider|||
|keep||determines which particles are kept for back-projection, -1 is one standard deviation worse than mean|spider|||
|xyshift||particles only allowed to shift this far from center|spider|||
|Approximate mass in Kd |||imagic|||