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On the Running tab, set: Number of MPI procsĪs the MPI nodes are divided between one leader (who does nothing else than bossing the others around) and two sets of followers who do all the work on the two half-sets, it is most efficient to use an odd number of MPI processors, and the minimum number of MPI processes for 3D auto-refine jobs is 3. (Set the id sequence of the GPU cards separated by colon ( 0:1:2) or leave it blank to automatically use all configured cards) Ignore the Helix tab, and on the Compute tab set: Use parallel disc I/O? You might want to check that you’re not loosing resolution for this in the later stages of your own processing, but during the initial stages it often does not matter much.) This will therefore speed up the calculations. (This will be more aggresive in proceeding with iterations of finer angular sampling faster. The only thing we will change here is to set: Use finer angular sampling faster? Only for higher symmetry refinements, we use 3.7 degrees sampling and perform local searches from 0.9 degrees. Therefore, for all refinements with less than octahedral or icosahedral symmetry, we typically use the default angular sampling of 7.5 degrees, and local searches from a sampling of 1.8 degrees. Note that the orientational sampling rates on the Sampling tab will only be used in the first few iterations, from there on the algorithm will automatically increase the angular sampling rates until convergence. On the Auto-sampling tab, one can usually keep the defaults. On the Optimisation tab set: Mask diameter (A):Īnd keep the defaults for the remaining options. (We typically start auto-refinements from low-pass filtered maps to prevent bias towards high-frequency components in the map, and to maintain the gold-standard of completely independent refinements at resolutions higher than the initial one.) Symmetry
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The optimisation set file shouldn’t contain a reference mask either as it’s been created after importing tomograms and coordinates.) (We’re not using a mask at this moment so leave this empty for now.
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InitialModel/job008/initial_model.mrc Reference mask (optional): (Note this is blank as it is extracted from the optimisation set file.) Reference map: (If an optimisation set file is provided, the input images STAR, reference map and solvent mask filenames are set based on its content, if not overrode below.) Input images STAR file: PseudoSubtomo/job007/optimisation_set.star On the I/O tab of the 3D auto-refine job-type set: Input optimisation set: Since the initial model was processed using pseudo-subtomograms with binning factor 4, we will start the 3D refinement using those same particles. However, as the pseudo-subtomogram files require more memory resources compared to SPA, we suggest to run this procedure in several steps, from high binning factors to 1, to improve processing time. it remains objective, and has been observed to yield excellent maps for many data sets.Īnother advantage is that one typically only needs to run it once, as there are hardly any parameters to optimize. Thereby, this procedure requires very little user input, i.e. Ĭombined with a procedure to estimate the accuracy of the angular assignments, it automatically determines when a refinement has converged. This procedure employs the so-called gold-standard way to calculate Fourier Shell Correlation (FSC) from independently refined half-reconstructions in order to estimate resolution, so that self-enhancing overfitting may be avoided. Once we have an initial reference map, one may use the 3D auto-refine procedure in relion to refine the dataset to high resolution in a fully automated manner.