REL 2016-06-02 2016-11-11 2016-11-11 0000-0002-8685-4896 Lu Gan Centre for BioImaging Sciences, Dept. of Biological Sciences, National University of Singapore 14 Science Drive 4 Singapore Singapore Singapore 117543 0000-0002-8685-4896 Lu Gan Centre for BioImaging Sciences, Dept. of Biological Sciences, National University of Singapore 14 Science Drive 4 Singapore Singapore Singapore 117543 Chen C Lim HH Shi J Tamura S Maeshima M Surana U Gan L 125.3 10.6019/EMPIAR-10062 EMDB EMD-8157 Chen C Lim HH Shi J Tamura S Maeshima K Surana U Gan L Molecular biology of the cell Mol. Biol. Cell 21 27 3357 3368 2016 English 10.1091/mbc.E16-07-0506 27605704 Tilt series of budding yeast cell cryosections and purified chromatin /data class averages MRC MRC 29 1 UNSIGNED 16 BIT INTEGER variable 5.8 variable 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