class averages

MRC

29

(None, None)

UNSIGNED 16 BIT INTEGER

(5.8, 5.8)

Tilt series data were acquired at various mags, resulting in either 5.8 or 8.9 Å pixel dimensions. Image width and height are variable.

# Budding yeast chromatin is dispersed in a crowded nucleoplasm in vivo
# Chen Chen, Hong Hwa Lim, Jian Shi, Sachiko Tamura, Kazuhiro Maeshima, Uttam Surana, Lu Gan
#
# IMOD reconstruction of yeast and chromatin cryotomograms
#
# Revised 20160417; IMOD version 4.8.47 3/17/2016
# This dir contains the minimal number of files needed to reconstruct the tomograms in Chen et. al.
# Note that some of the tomograms need to be binned x2 to facilitate visualization.
1) Make a .st file from the .mrc tilt series and place in the correct dir (see details below).
2) Run etomo from that directory:
etomo 14oct01a__014.edf
3) In etomo, execute only the following commands.
Final Aligned Stack: (Create Tab) Create Full Aligned Stack
(Correct CTF Tab) Select the right Falcon noise file, Correct CTF, Use CTF Correction
(2D Filter Tab) Filter, Used Filtered Stack, Done
Tomogram Generation: Generate Tomogram, Done
Post-processing : Trim Volume, Done
Clean Up : optional cleanup, Done

Create .st files as follows:

# The following use the Falcon2_20141217 noise files for CTF correction
newstack -secs 1-61 14oct01a__014.mrc 14oct01a__014.st
newstack -secs 0-47 14oct01a__021.mrc 14oct01a__021.st
newstack 14oct01a__027.mrc 14oct01a__027.st
newstack 14oct01a__032.mrc 14oct01a__032.st
newstack -secs 2-59 14oct01a__052.mrc 14oct01a__052.st
newstack -secs 0-60 14oct01a__067.mrc 14oct01a__067.st

# The following use the Falcon2_20150328 noise files for CTF correction
newstack 15apr11_chrom_01.mrc chrom_01.st
newstack 15apr11_chrom_02.mrc chrom_02.st
newstack 15apr29_chrom_15.mrc chrom_15.st
newstack 15apr29_chrom_32.mrc chrom_32.st
newstack -secs 0-58 15mar02a__046.mrc 15mar02a__046.st
newstack 15mar02a__065.mrc 15mar02a__065.st
newstack 15mar02a__070.mrc 15mar02a__070.st
newstack -secs 0-59 15mar02a__074.mrc 15mar02a__074.st
newstack 15may05_chrom_07.mrc chrom_07.st
newstack 15may29_chrom_11.mrc chrom_11.st
newstack 15may29_chrom_15.mrc chrom_15.st
newstack 15may29_chrom_19.mrc chrom_19.st
newstack 15may29_chrom_21.mrc chrom_21.st
newstack 15oct12_yeast_02.mrc yeast_02.st
newstack 15oct12_yeast_03.mrc yeast_03.st
newstack 15oct12_yeast_04.mrc yeast_04.st
newstack 15oct12_yeast_12.mrc yeast_12.st
newstack 15oct12_yeast_15.mrc yeast_15.st
newstack 16jan29_yeast_01.mrc yeast_01.st
newstack 16jan29_yeast_05.mrc yeast_05.st
newstack 16jan29_yeast_09.mrc yeast_09.st
newstack 16jan29_yeast_10.mrc yeast_10.st
newstack 16jan29_yeast_17.mrc yeast_17.st

Download #files