Notes

• The following list will not be exhaustive.
• Headers may not match outputs exactly, but should be equivalent.

params

• Created by: make-params.spi
• Used by: many batch files
• The Reconstruction parameters file

;              MICROGRAPH 

sel_micrograph

• Created by: mkfilenums.py montagefromdoc.py

;       TRANSFER      R,PX^-1      R,A**-1

1. Power_Spectra/power/filtctf{****[mic-num]}
• Created by: trapctf.spi
• Used by: filtctf.spi
2. Reconstruction/docmatched_vol001
• Created by: make_matched.spi
• Used by: matchedfilter.spi

;               XCOORD       YCOORD       MIC_SLICE   PEAK_HEIGHT 

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

• Created by: lfc_pick.spi
• Used by: eman2spider.spi, rewindow.spi

;       MIC_SLICE    GLOBALPART

Particles/good/ngood{****[mic-num]}

• Created by: numberparticles.spi
• Used by: filtctf.spi, group_particles.spi, goodpartsbymic.spi
• Column GLOBALPART not required or used downstream

; KEY:MIC_SLICE /  GLOBAL_PARTICLE_NUM 

Particles/win/globalmic{****[mic-num]}

• Created by: numberparticles.spi
• Used by: group_particles.spi, stackcombine.spi

;        APSHSLICE     MIC_SLICE     APSHGROUP      MICNUM       GLOBALNUM 

Alignment/apsh_grp_particles_{***[group-num]}

• Created by: group_particles.spi
• Used by: apsh-settings.spi, bestim.spi

; KEY=GLOBAL / GRPSLICE     MICSLICE     GROUPNUM    MICROGRAPH

Alignment/global2group

• Created by: group_particles.spi
• Used by: goodpartsbymic.spi, selectbyview.spi

;                   PSI,        THE,         PHI,         REF#,       EXP#,     CUM. {INPLANE,    SX,         SY},        NPROJ,        DIFF,       CCROT,      INPLANE,        SX,         SY,         MIR-CC

Alignment/align_01_{***[grp]}

• Created by: apsh-settings.spi
• Used by: selectbyview.spi, stackcombine.spi, bps-settings.spi
• See Note #1 in the 'AP SH' documentation for a more detailed description.

; /     VIEWSLICE   GLOBAL_NUM    GRPSLICE      CC_ROT       MIRROR      GROUPNUM       VIEW

1. Averages/Views/sel{***[view-num]} created by: selectbyview.spi
• avgfilterbyview.spi
• classifybyview.spi
• combinegoodclasses.spi
2. Averages/Views/prj{***[view-num]}/sortsel created by: selectbyview.spi
   Used by:
• histallcc.spi
• recheck.spi
• bestim.spi
3. Averages/combinedparts created by: histallcc.spi
4. Reconstruction/select/prj{***[view-num]}/goodsel created by: combinegoodclasses.spi
   Used by:
• histgoodcc.spi
• recheck.spi
• bestim.spi
5. Averages/combinedgood
• Created by: histgoodcc.spi
• Used by: goodpartsbymic.spi
6. Averages/Views/bestsel{***[view-num]}
• Created by: bestim.spi
• Used by: stackcombine.spi

;       VIEWSLICE    GLOBAL_PART    CC_COEFF        CCROT      MIRROR_FLAG     GRP_NUM      GRP_SLICE

Averages/Views//prj{***[view-num]}/docclass{***[class-num]}

• Created by: classifybyview.spi
• Used by: combinegoodclasses.spi

;       CLASSNUM       CCC        VARIANCE_SD 

Averages/Views//prj{***[view-num]}/listclasses

• Created by: classify.spi
• Used by: verifybyview.py

;      NORM'D FREQ    DPR        FSC        FSCCRIT     VOXELS

Groups/grp{***[grp]}/doccmp001, doccmp001
Groups/grp{***[grp]}/docfscmasked001, docfscmasked001

• Created by: bps-settings.spi
• Used by: plotres.spi
• See Note #1 in the 'RF 3' documentation for a more detailed description.

(Updated 2012 May 21)