(Updated 2012 May 21) MAY BE OUT-OF-DATE

Doc file formats

Notes

• The following list will not be exhaustive.
• Headers may not match outputs exactly, but should be equivalent.
• Legacy documentation -- MAY BE OUT-OF-DATE.

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params.dat

• CREATED BY: makeparams.spi
• USED BY: Many batch files
• See reconstruction parameters for a detailed description

sel_micrograph

;   MICROGRAPH 

• CREATED BY: mkfilenums.py
• USED BY: Many batch files, montagefromdoc.py

Power_Spectra/def_avg <

;   MICROGRAPH    DEFOCUS      DF_GROUP    AVGDEFOCUS 

• CREATED BY: defavg.spi
• USED BY: dfgoodapsh.spi

../batch/Particles/coords/sndc{****[mic-num]}

;         XCOORD       YCOORD      MICSLICE     PEAK_HT 

• CREATED BY: lfc_pick.spi or eman2spider.spi
• USED BY: rewindow.spi

../batch/Particles/coords/ngood{****[mic-num]}

;       MIC_SLICE    GLOBAL_PART 

• CREATED BY: particles.spi
• USED BY: sel_by_group.spi, win2stk.spi (in lieu of ngood****)

../batch/Particles/coords/mic2global{****[mic-num]}

; KEY=MIC_SLICE /  COLUMN1=GLOBAL_PART    

• CREATED BY: numberparticles.spi
• USED BY: selectbyviewall.spi, regroup.spi

Alignment/sel_../batch/Particles_{***[group-num]}

;        DF_SLICE     MICSLICE     DF_GROUP    MICROGRAPH 

• CREATED BY: sel_by_group.spi
• USED BY: selectbyviewall.spi, regroup.spi

Reconstruction/sel_group{,_cclim,_cclim_sorted}

;        DF_GROUP     NUMPARTS    AVGDEFOCUS 

• sel_group created by sel_by_group.spi
• sel_group_{cclim,cclim_sorted} created by goodparticlesbydf.spi
• USED BY: Many batch files

Alignment/align_01_{***[df-group]}

;                   PSI         THETA         PHI       REF_PROJ     DF_SLICE     IN_PLANE    CUM_XSHIFT   CUM_YSHIFT    NUM_PROJ      ANGDIF       CC_ROT    CURR_INPLANE CURR_XSHIFT  CURR_YSHIFT     MIRROR 

• CREATED BY: apshgrp.spi
• USED BY: Many batch files
• See Note #1 in the 'AP SH' documentation for a more detailed description.

Reconstruction/stack2particle{***[df-group]}

;      GLOBAL_PART   MICROGRAPH    MICSLICE     DF_SLICE 

• CREATED BY: selectbyviewall.spi or regroup.spi
• USED BY: goodparticlesbydf.spi, reselect_byview.spi

Reconstruction/select/sel{***[view-num]}

;       VIEW_SLICE  GLOBAL_PART    DF_SLICE      CC_ROT       MIRROR      DF_GROUP       VIEW 

• CREATED BY: selectbyviewall.spi
• USED BY: filterbyview.spi, classify.spi, combinegoodclasses.spi, reselect_byview.spi

Reconstruction/df{***[df-group]}/select/sel{***[view-num]}

;        DF_SLICE      CC_ROT       MIRROR 

• CREATED BY: selectbyviewall.spi
• USED BY: select.spi, bestim.spi

Reconstruction/select/prj{***[view-num]}/docclass{***[class-num]}

;       VIEW_SLICE  GLOBAL_PART      CCC         CC_ROT       MIRROR      DF_GROUP     DF_SLICE 

• CREATED BY: classify.spi
• USED BY: combinegoodclasses.spi

Reconstruction/select/prj{***[view-num]}/listclasses

;       CLASSNUM       CCC        VARIANCE_SD 

• CREATED BY: classify.spi
• USED BY: verifybyview.py, byhand2goodclasses.spi

Reconstruction/select/prj{***[view-num]}/goodsel

;       VIEW_SLICE  GLOBAL_PART    DF_SLICE      CC_ROT       MIRROR      DF_GROUP       VIEW 

• CREATED BY: combinegoodclasses.spi
• USED BY: recheck.spi, histgoodccc.spi

Reconstruction/combinedgood.dat

;       VIEW_SLICE  GLOBAL_PART    DF_SLICE      CC_ROT       MIRROR      DF_GROUP       VIEW 

• CREATED BY: histgoodccc.spi
• USED BY: goodparticlesbydf.spi, regroup.spi

Reconstruction/df{***[df-group]}/goodparticles

;        DF_SLICE   GLOBAL_PART     CC_ROT 

• CREATED BY: goodparticlesbydf.spi
• USED BY: dfgoodapsh.spi

Reconstruction/sel_../batch/Particles_{***[group-num]}

;        DF_SLICE     MICSLICE     DF_GROUP    MICROGRAPH   GLOBAL_PART 

• CREATED BY: dfgoodapsh.spi or regroup.spi
• USED BY: bestim.spi, bps-by-df.spi, consecprepare.spi

df***/doccmp001, doccmp001, df***/docfscmasked, docfscmasked

;      NORM'D FREQ    DPR        FSC        FSCCRIT     VOXELS

• CREATED BY: bps-settings.spi
• USED BY: plotres.spi
• See Note #1 in the 'RF 3' documentation for a more detailed description.