6. Reconstruct tomogram
Doppio has a wrapper around the RELION tomogram reconstruction job. To run this job, go to NEW JOB tab in Doppio GUI and find the Reconstruct and choose RELION Reconstruct Tomogram job.
The job parameters are explained in the Relion documentation below. In the image below, we show the job parameters we used for the tutorial data. The dimensions of the resulting tomogram(s) is controlled by the Xdim, Ydim, Zdim parameters in combination with the Binned pixel size parameter. Note the Xdim, Ydim and Zdim should be given in unbinned pixels. Xdim and Ydim have chosen to be 4000 which is slightly larger than the recorded image size (3710 x 3838). The Zdim is chosen to include the full thickness of the sample plus some extra margin. It may be necessary to adjust these parameters depending your interest area in the tomogram. The Binned pixel size 10 A is a reasonable choice for most tomograms, but you may want to adjust it depending on your needs. For example, if you’re interested in Ribosomes, even 15 A binned pixel size would be sufficent. However, if you’re interested in smaller complexes, you may want to use smaller unbinned pixel size to avoid averaging them out in the noise. The sampling in the resulting tomogram is given by
Note also that we haven’t asked to generate half-tomograms for denoising because the data quality is good enough to pick particles directly from the tomograms. However, if you plan to do denoising using RELION’s denoising tool, you should enable the half-tomogram option here.
Once the job is finished, the output can be found in the Tomograms/job006/ directory. The reconstructed
tomograms are inside the tomograms/ sub-directory in mrc format.
You can visualize the tomograms using the Doppio image viewer.
For more details about the RELION tomogram reconstruction job, please refer to the RELION documentation below.