How to download the cryo-em files

Getting map symmetry We will want a symmetry file describing the symmetry operators that have been used in our map. We can get them automatically in about 30 seconds with:. The model is mostly pretty good but may need some fixing, depending on your version of Phenix. If you look at this model in Coot or Chimera you'll see it has moved some side chains into density, but that the model still doesn't match the density for residues NOTE: the results for these steps may depend on platform, version, and number of processors so you may have to adjust them based on what your model looks like.

Redo the sequence assignment and see if we can fill in the gap. The model should fit the map quite well. If there are missing side chains, you can fill them in with:. You could refine once more too:.

Next you would go over the model carefully using validation tools and remove any parts that are not ok and fix parts that are not quite right. You can also create the full mer using your map symmetry and the model. Tutorial: Solving a structure with cryo-EM data using model-building This example is density modification of a cryo-EM map, followed by structure determination by automatic model-building, fixing a mis-traced segment, sequence assignment and refinement NOTE: the details of what needs to be fixed after automatic model-building steps may change with platform, number of processors or version of Phenix used The data are half-maps for apoferritin EMD entry , 1.

We can get them automatically in about 30 seconds with: phenix. It is also advisable to read through relevant sections of the Tomography Guide before trying to process your own tilt series. If you have processed a tilt series in Etomo before, you may want to do the dual-axis tutorial before this example, especially if you have difficulty following the steps below without shots of how the screen should appear. First, a few points on conventions: labels in the Etomo or 3dmod interface are shown in Bold , and entries in fields are shown in italics.

For mouse operations in the Zap window in 3dmod, the buttons are referred to as "first", "second", and "third" because the buttons can be remapped in 3dmod. If you have not changed the mapping, this corresponds to left, middle, and right; otherwise, it refers to whatever you have chosen to be the first, second, and third buttons.

In this initial step, we define some features of the data set and create the files needed for processing. This step is needed to remove artifacts in the images, generally produced by X-ray events in the camera. These artifacts will produce streaks in a reconstruction and can also make it harder to see the image features, which have a much smaller dynamic range than the artifacts. In this step, we use image cross-correlation to align successive images, which makes it easier to track fiducial markers.

In this step, the positions of selected gold markers are found on all of the images, which allows a more accurate alignment to be obtained. Next the bead positions are fit to a mathematical model of specimen movements. The model predicts a position for each bead on each view, and the mean distance between the predicted and actual positions is referred to as the "mean residual error". These errors will let you find and correct badly modeled points.

The need to do so has been much reduced by the recent addition of a method called "robust fitting", which automatically gives less weight or even eliminates the points most likely to be at incorrect positions.