Journal of Structural Biology

Script 1. Automatic coma determination program. Data was collected using the apo-ferritin sample with a continuous carbon-film grid at -2um defocus value. It is necessary to eliminate the original astigmatism and coma in manual before measurement to get original beam tilt angles (ori_X and ori_Y). Script 2. Coma search of beam-image shift. Run script 2 and record changes of astigmatism and coma in different α and d. The changes of astigmatism obtain from the Stigmator window of serialEM and coma obtain via automatic coma determination program. Fit all the parameters to get the fitting curves and formulas which are applied to the beam-image shift data collection. Script 3. 6×6 data collection via beam-image shift. In theory, only to know α0 and r (Figure 3), we can calculate all the parameters needed for data collection. But there is a slight difference between the actual and theoretical values due to the error in grid production or other objective factors.

These are electron cry-tomograms associated with the manuscript

This is the refined X-ray crystal structure of an internal deletion of monomeric sulfite reductase flavoprotein with an internal truncation that allowed us to determine the structure of each domain in the same structure.

The ability to rapidly assess microtubule number in 3D image stacks from electron tomograms is essential for collecting statistically meaningful data sets. Here we implement microtubule tracing using 3D template matching. We evaluate our results by comparing the automatically traced centerlines to manual tracings in a large number of electron tomograms of the centrosome of the early Caenorhabditis elegans embryo. Furthermore, we give a qualitative description of the tracing results for three other types of samples. For dual-axis tomograms, the automatic tracing yields 4% false negatives and 8% false positives on average. For single-axis tomograms, the accuracy of tracing is lower (16% false negatives and 14% false positives) due to the missing wedge in electron tomography. We also implemented an editor specifically designed for correcting the automatic tracing. Besides, this editor can be used for annotating microtubules. The automatic tracing together with a manual correction significantly reduces the amount of manual labor for tracing microtubule centerlines so that large-scale analysis of microtubule network properties becomes feasible.