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
