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Tapu Shaikh edited this page Oct 6, 2023 · 7 revisions

Outputs

Grouped by directory

Run directory

  • log-snartomo.txt – specific for SNARTomoClassic
    • contains all screen output (except in the case of --testing or --verbosity=0)
    • filename can be overridden by --log_file

Top-level output directory

  • commands.txt
    • contains the command line(s) that were used for runs sent to this output directory
    • If multiple runs specified the same output directory, the command lines will be appended.
    • useful for bookkeeping
    • NOTE: Quotes do NOT appear in this file (a BASH limitation). If you copy & paste a command from here, remember to restore them around space-delimited lists and around strings containing wild cards.
  • settings.txt
    • contains settings – both user-specified and default – for last run
    • also repeated at the top of the log file
  • GAIN_REFERENCE.mrc – if input gain reference wasn’t in MRC format, the MRC version will be here

Logs

This directory is only used with SNARTomoPACE.

  • snartomo.txt – Record of the screen output (except for the counters)
  • files.txt – Record of each operation on a movie/micrograph or tomographic reconstruction
  • motioncor2.txt – Screen output from MotionCor2
  • ctffind4.txt – Screen output from CTFFIND4
  • recon.txt – Screen output for operations on each tilt series
  • Resource logs
    • log-gpu.txt – Log of GPU memory
    • plot-gpu.gnu – Plot of GPU memory: gnuplot --persist plot-gpu.gnu
    • log-mem.txt – Log of system memory (RAM)
    • plot-mem.gnu – Plot of system memory: gnuplot --persist plot-mem.gnu
    • log-power.txt – Log of GPU power consumption
    • plot-power.gnu – Plot of GPU power consumption: gnuplot --persist plot-power.gnu
    • log-heat.txt – Log of GPU temperature
    • plot-heat.gnu – Plot of GPU temperature: gnuplot --persist plot-heat.gnu

0-Movies

This directory is only used with SNARTomoClassic.

  • Movie files will be moved here. Moving the files was the easiest way to keep track of which files have been processed already.
  • If you need to resume a SNARTomoClassic run, add the flag --restore_movies. SNARTomo will move the movies back to the input directory so that it can assign them to their respective tilt series. (MotionCor2 and CTFFIND4 will not be re-executed.)

1-Compressed

  • *.tif – EERs optionally compressed into TIFF format (refer to the --grouping parameter for more information)

2-MotionCor2

  • *_mic.mrc – Non-dose-weighted motion-corrected micrographs
  • Logs/*mic.out – screen output from MotionCor2
  • Logs/*Full.log – shift parameters for each frame
  • Logs/*Tiff.log – list of micrographs processed (will be a single micrograph in on-the-fly mode)

3-CTFFIND4

  • SUMMARY.CTF
    • summary of CTF fits for all micrographs – extracted from *_ctf.txt files
    • Each tomogram directory (below) will contain the corresponding subset.
    • Columns:
      • 0: micrograph name
      • 1: micrograph number (1 in on-the-fly mode)
      • 2: defocus along minor axis
      • 3: defocus along major axis
      • 4: angle of astigmatism (azimuth)
      • 5: phase shift (not used for us)
      • 6: correlation value
      • 7: estimated resolution of fitting
  • *_ctf.txt – fitting summary for each micrograph
  • *_ctf.mrc – power spectra, experimental and fitted
  • *_ctf.out – screen output from CTFFIND4
  • *_ctf_avrot.pdf – 1D profiles, plotted, of experimental and fitted power spectra
  • *_ctf_avrot.txt – 1D profiles, as text

4-Denoised

  • *_mic.mrc – Denoised, non-dose-weighted motion-corrected micrographs

5-Tomo

Each tilt series will generate its own subdirectory. The outputs will different depending on whether you computed the reconstruction using AreTomo (the default) or IMOD (using the --batch_directive flag).

Both AreTomo & eTomo

For each tilt series, a new subdirectory will be created. In each such subdirectory, there will be a file called *snartomo.log which contains screen output for the following steps:

  • dose-fitting
  • CTF plots for each tilt series (ctfbyts.py)
  • newstack command lines
  • summary of 3D reconstruction output
  • extraction of central section

AreTomo

  • *.rawtlt – tilt angles, sorted from lowest (most negative) to highest
  • *.imod.txt – list of micrographs – needed by IMOD
  • *_newstack.mrc – tilt-series micrographs, ordered from lowest angle (most negative) to highest
  • *_newstack.log – output from IMOD’s newstack
  • *_newstack.aln – alignment parameters
  • *_newstack.xf – other (??) parameters
  • *_aretomo.mrc – tomographic reconstruction
  • *_aretomo.log – screen output from AreTomo

eTomo

UNDER CONSTRUCTION

Root name for each tomogram is assumed here to be called “TOMO_ROOT”.

  • *.mrc.mdoc.orig – MDOC containing all images (before dose-fitting)
  • SUMMARY_CTF.txt – CTFFIND4 parameters for micrographs in current tilt series
  • TOMO_ROOT_ctfs.txt – list of CTFFIND4 power spectra, in format needed for newstack command
  • TOMO_ROOT_ctfstack.mrcs – MRC stack of CTFFIND4 power spectra
  • TOMO_ROOT.mrc.mdoc – MDOC containing retained images (after dose-fitting)
  • TOMO_ROOT_dose.txt – dose for each micrograph in tilt series, as reported in MDOC file
  • TOMO_ROOT_dosefit.log – summary of dose-fitting, including residuals, and whether micrograph was removed
  • TOMO_ROOT_newstack.rawtlt – tilt angles, sorted from most negative to most positive
  • TOMO_ROOT_goodangles.txt – indices for retained micrographs, sorted by tilt angle (most negative to most positive)
  • TOMO_ROOT_mcorr.txt – list of retained unfiltered micrographs, in format needed for newstack command
  • TOMO_ROOT_denoise.txt – list of retained denoised micrographs (optional), in format needed for newstack command
  • TOMO_ROOT_newstack.mrc – original tilt-series stack
  • TOMO_ROOT_newstack.log – screen output of newstack
  • batchDirective.adoc – copy of input batch directive
  • TOMO_ROOT_newstack_preali.mrc – unaligned tilt series, downsampled
  • TOMO_ROOT_newstack_ali.mrc – tilt series, downsampled and aligned, tilt axis vertical
  • TOMO_ROOT_newstack_rec.mrc – 3D reconstruction, reoriented
  • TOMO_ROOT_newstack_full_rec_slice.mrc – central slice through reconstruction
  • TOMO_ROOT_newstack_full_rec_slice_norm.jpg – central slice through reconstruction, normalized, JPEG format
  • etomo_out.log
  • etomo_err.log
  • ctfplotter.com
  • eraser.com
  • ctfcorrection.com
  • xcorr.com
  • prenewst.com
  • track.com
  • TOMO_ROOT_newstack.seed
  • mtffilter.com
  • tomopitch.com
  • sample.com
  • TOMO_ROOT_newstack_peak.mod
  • eraser.log
  • TOMO_ROOT_newstack_fixed.st.stats.log
  • TOMO_ROOT_newstack_xray.mrc.gz
  • archiveorig.log
  • xcorr.log
  • TOMO_ROOT_newstack.prexf
  • TOMO_ROOT_newstack.prexg
  • prenewst.log
  • xcorr_pt.com
  • origcoms
  • dfltcoms
  • TOMO_ROOT_newstack_pt.fid
  • xcorr_pt.log
  • TOMO_ROOT_newstack.fid
  • align.com
  • TOMO_ROOT_newstack.xtilt
  • TOMO_ROOT_newstack.tltxf
  • TOMO_ROOT_newstack.tlt
  • TOMO_ROOT_newstack.resid
  • TOMO_ROOT_newstackfid.xyz
  • TOMO_ROOT_newstack.3dmod
  • TOMO_ROOT_newstack_fid.xf
  • TOMO_ROOT_newstack.xf
  • TOMO_ROOT_newstack_fid.tlt
  • TOMO_ROOT_newstack.resmod
  • align.log
  • taMappings.log
  • taError.log
  • taSolution.log
  • taLocals.log
  • taCoordinates.log
  • taAngles.log
  • taBeamtilt.log
  • taRobust.log
  • newst.com
  • newst.log
  • tilt.com
  • TOMO_ROOT_newstack_full_rec.mrc
  • tilt.log
  • processchunks.out
  • TOMO_ROOT_newstack.edf
  • batchruntomo.log
  • trimvol.log

Images

Central sections

In the Images/Thumbnails subdirectory, a central section will be saved in JPG format for each reconstruction.

DoseDiscriminator

In the Images/Dosefit subdirectory, the results of dose-fitting are plotted.

Color code:

  • green: points passing minimum and residual criteria
  • orange: points passing minimum criterion but not residual criteion
  • blue: points below minimum threshold

See the “Parameters” section above to see how to adjust these threshold parameters.

CTF plot

Below is an example of the output of ctfbyts.py, called ctfbyts.png in the Images directory.

Each column represents the data for each tilt series. The earliest images in the tilt series are colored in blue, and the later images are colored in yellow.

The top panel is the fitted resolution, as determined by CTFFIND4. The units on the left vertical axis (x1-axis) are reciprocal Angstroms, and in simple Angstroms on the right (x2). As the dose increases, and as the tilt increases, the fitted resolution gets worse.

The second panel down is CTFFIND4’s “CCFit” value. As the dose increases, and as the tilt increases, the correlation gets worse.

The third panel down is CTFFIND4’s estimated defocus value. As the dose increases, and as the tilt increases, the estimated defocus deviates more from the desired defocus.

It may be uninteresting to observe the data for the later images. To plot only the first (for example) 15 micrographs, add --ctfplot_first 15 flag to the SNARTomo command line.

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