File name conventions

Data collection on Titan Krios, run by SerialEM.

Table of Contents Raw movies are called: Copied into 2dx as: Files after the unpack script: Files after the drift correction script: Files after the 2dx intialize files script: Files after the 2dx CTF Correction (Part 1) script: Files after the 2dx Unbending script:

Raw movies are called:

File names	Variable names	Example contents	Type
oriname.tif	imagename_original (path)	/home/myfolder/PS2_00001_Sep22_18.10.51.mrc	TIFF, LZV compressed, 3838x3710x80
Gainreference.dm4	gainref_original (path)	/home/myfolder/CountRef_TssA_Sep28_15.27.14.dm4	DM4 file, 3838x3710x1
Countdefects.txt	defects_original (path)	/home/myfolder/CountDefects_TssA_Sep28_15.27.14.txt	ASCII list of defect pixels (?)

Copied into 2dx as:

File names	Variable names	Example contents	Type
oriname.mrcs	import_rawstack	PS2_00001_Sep22_18.10.51.mrcs	MRC, 3838x3710x80
Gainreference.dm4	import_gainref	CountRef_TssA_Sep28_15.27.14.dm4	DM4 file, 3838x3710x1

Files after the unpack script:

File names	Variable names	Example contents	Type
raw_gaincorrectedstack.mrcs	raw_gaincorrectedstack	raw_gaincorrectedstack	MRC, 3838x3710x80
raw_gaincorrectedstack.mrc			MRC, 3838x3710x1
raw_gaincorrectedstack_fft.mrc			MRC, 3838x3710x1

Files after the drift correction script:

File names	Variable names	Example contents	Type
movie_aligned.mrcs	movie_stackname	movie_aligned	MRC, 3838x3710x80
movie_aligned.mrc			MRC, 3838x3710x1
movie_aligned_fft.mrc			MRC, 3838x3710x1
translations.png			PNG file (drift trajectory figure)
CTFDiag.png			PNG file (CTF Thonring fit figure)

Files after the 2dx intialize files script:

File names	Variable names	Example contents	Type
image_2dx.mrc	nonmaskimagename	PS2_00001_Sep22_18_10_51	MRC, 3840x3840x1 (square)
mimage_2dx.mrc	imagename	mPS2_00001_Sep22_18_10_51	MRC, 3840x3840x1 (square)

Files after the 2dx CTF Correction (Part 1) script:

File names	Variable names	Example contents	Type
ThonRingFit.mrc			MRC, 400x400x1
image_ctfcor.mrc			MRC, 3840x3840x1

Files after the 2dx Unbending script:

File names	Variable names	Example contents	Type
ManualMasking_UnbendPlot.mrc			MRC (Unbending profile figure)
IQplot.mrc			MRC (IQ Plot figure)