7. 3D Map preprocessing
The Fig. 7.1 shows the workflow that we are going to detail in this section.
7.1. Map sharpening
7.2. Comparison of maps
Realize that at this point we have generated two optimized maps derived from the initial one. Additionally, some other maps could have been obtained using other map optimization methods. A comparison among them would be interesting to consider which one(s) of them should be used as input in next steps of modeling workflow. The ideal map for tracing the atomic structure should include as many details and connections as possible and, at the same time, preserve the density areas of the initial map. In other words, we can use the best sharpened map (with higher resolution) corroborating that it does not make up new densities, absent in the starting map. Nevertheless, selecting “the best” sharpened map could be difficult sometimes, especially if the map is very big or there are some regions optimized in one of the sharpened maps and other areas optimized in the other one. In that case, you can use several maps at the same time, having all of them perfectly aligned according to the same origin of coordinates.
In the tiny example shown in this tutorial we are working with a high resolution map and there are almost no differences in resolution between the starting map and the two derived sharpened maps, although this is not usually the case in real life. In this quite uncommon case the initial unsharpened map would be enough to trace the atomic structure. However, in order to detail the method, the starting map and their two sharpened ones will be used simultaneously.
7.3. Extraction of the asymmetric unit map
After executing the protocol (Fig. 7.12 (9)), the resulting expanded ASU can be observed (10) with ChimeraX (Fig. 7.13). Note the additional expanded volume of the ASU on the left side of the figure. The ASU itself, on the right side, constitutes the half volume. Since the total volume contains the structure of four proteins, we can anticipate that this smaller asymmetrical subunit of the initial volume contains two proteins, one \alpha and one \beta subunit. Then, the respective structures of these two proteins could be fitted in the map ASU simultaneously or in successive modeling workflow steps.