Reconstruction Parameters » History » Version 34
Amber Herold, 05/31/2011 03:25 PM
1 | 1 | Amber Herold | h1. Reconstruction Parameters |
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4 | 19 | Amber Herold | |_.Name|_.a.k.a.|_.Description|_.Used By|_.Make common to all?|_.Notes| |
5 | 25 | Amber Herold | |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|| |
6 | 23 | Amber Herold | |Inner Mask Radius|Inner Radius,Particle inner mask radius|inner radius for alignment in pixels|xmipp, frealign, spider|y|not xmipp| |
7 | 24 | Amber Herold | |Outer Alignment Radius|||xmipp, eman, imagic|y|not eman, frealign| |
8 | |Inner Alignment Radius|||xmipp, eman, imagic|y|not eman, frealign| |
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9 | 21 | Amber Herold | |Symmetry Group|sym|ex. c1, c2...|xmipp,eman,frealign,spider,imagic|y|| |
10 | |Number of iterations|iteration number||xmipp|y|| |
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11 | |Angular Sampling Rate|ang|angular step for projections in degrees|xmipp,EMAN|y|not frealign| |
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12 | |Percentage of worst images to discard|||xmipp|y|not frealign| |
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13 | 29 | Amber Herold | |Filter reconstructed volume to estimated resolution|flt3d|||y|not frealign| |
14 | |Filter reconstructed volume to resolution computed by fsc|Low Pass Filter the reference?, Constant to add to the estimated resolution|||y|not frealign, eman| |
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15 | 31 | Amber Herold | |Last particle to use|||frealign|y|specific to stack preparation, not refinement alg| |
16 | |lp|filtering|low pass filter in angstroms|spider, imagic|y|specific to stack preparation, not refinement alg| |
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17 | |hp|filtering|high pass filter in angstroms|spider, imagic|y|specific to stack preparation, not refinement alg| |
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18 | 1 | Amber Herold | ||||||| |
19 | 22 | Amber Herold | |imask||radius of internal mask (in pixels for eman and spider, Angstroms for frealign)|EMAN||| |
20 | 10 | Amber Herold | |amask||amask=[r],[threshold],[iter]|eman||| |
21 | 1 | Amber Herold | |Mask Filename|||xmipp||| |
22 | 10 | Amber Herold | |Max angular change|||xmipp||| |
23 | |max change offset|||xmipp||| |
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24 | 19 | Amber Herold | |Search range for 5d transitional search|||xmipp||| |
25 | 1 | Amber Herold | |Reconstruction Method|||xmipp||| |
26 | 10 | Amber Herold | |Values of lambda for ART|||xmipp||| |
27 | |Initial max frequency used by reconstruct fourier|||xmipp||| |
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28 | |Compute resolution?|||xmipp||don't need this, should always be set to yes| |
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29 | |maxshift||max translation during image alignment in pixels|eman||| |
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30 | |hard||hard limit for make3d program|eman||| |
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31 | |clskeep||=[std dev multipier] how many raw particles discarded for each class average|eman||| |
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32 | |clsiter||iterative alignmnet to each other|eman||| |
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33 | |xfiles||=[mas in kD]|eman||| |
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34 | |shrink||scale down by a factor of [n] before classification|eman||| |
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35 | |euler2||=[oversample factor]|eman||| |
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36 | |median||use median value instead of average for each pixel|eman||| |
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37 | |phscls||use signal to noise ratio weighted phase residual|eman||| |
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38 | |refine||do subpixel alignment|eman||| |
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39 | |tree||decimate reference populatiuon|eman||| |
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40 | |coran||use coran algorithm|eman||| |
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41 | 30 | Amber Herold | |eotest||use even odd test|eman||remove this, should always be yes, takes place of Compute Resolution?| |
42 | 10 | Amber Herold | |amplitude contrast (WGH)|||frealign||| |
43 | |Standard deviation filtering|||fealign||| |
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44 | |Phase B-factor weighting constant (PBC) |||frealign||| |
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45 | |B-factor offset (BOFF) |||frealign||| |
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46 | |Number of randomized search trials (ITMAX) |||frealign||| |
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47 | |Number of potential matches to refine (IPMAX)|||frealign||| |
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48 | |Target phase residual (TARGET) |||frealign||| |
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49 | |Worst phase residual for inclusion (THRESH)|||frealign||| |
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50 | |Resolution limit of reconstruction (RREC) (in Ångstroms; default Nyquist) |||frealign||| |
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51 | 32 | Amber Herold | |Lower resolution limit or high-pass filter (RMAX1) (in Ångstroms) |||frealign||? is this the same as stack prep lp/hp filter| |
52 | |Higher resolution limit or low-pass filter (RMAX2) (in Ångstroms; default 2*Nyquist) |||frealign||? is this the same as stack prep lp/hp filter| |
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53 | 1 | Amber Herold | |B-factor correction (RBFACT) (0 = off)|||frealign||| |
54 | 27 | Amber Herold | |Only use CTFFIND values|||frealign||| |
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56 | 1 | Amber Herold | |MSA - num class averges to produce from raw images|||imagic||| |
57 | |MSA - num factors to use for classification|||imagic||| |
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58 | |MSA - percentage of worst class members to ignore after classification|||imagic||| |
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59 | |threed reconstruction||object size, low-pass filter 3d volume|imagic||| |
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60 | |Center stack prior to alignment |||imagic||| |
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61 | |Mirror references for alignment |||imagic||| |
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62 | 12 | Amber Herold | |MRA - min radius for rotational alignment in pixels|||imagic||| |
63 | |MRA - max radius for rotational alignment in pixels|||imagic||| |
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64 | 1 | Amber Herold | |MSA - fraction of final class averages to keep|||imagic||| |
65 | |MRA - angular increment of forward projections|||imagic||| |
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66 | |MRA - max radial shift compared to original images|||imagic||| |
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67 | |MRA - max radial shift during this iteration|||imagic||| |
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68 | |MSA - percentage of images to ignore when calculating eiganimages|||imagic||| |
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69 | |Angular reconstitution||angular increment of forward projections, ang inc of euler search, fraction of best ordered images to keep|imagic||| |
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70 | 33 | Amber Herold | |firstring|similar to alignment radius|Any pixels this far away from center will not be used|spider||| |
71 | |lastring|similar to alignment radius|Only pixels this far away will be used|spider||| |
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72 | 13 | Amber Herold | |xysearch||translational search during projection matching will be limited to this many pixels from the center ofthe image|spider||| |
73 | 34 | Amber Herold | |angular increments|Angular Sampling Rate|list of angular increments for projection mapping|spider||| |
74 | 13 | Amber Herold | |keep||determines which particles are kept for back-projection, -1 is one standard deviation worse than mean|spider||| |
75 | 1 | Amber Herold | |xyshift||particles only allowed to shift this far from center|spider||| |
76 | 14 | Amber Herold | |Approximate mass in Kd |||imagic||| |