10. Merging 3D Maps and Atomic Structures: Rigid Fitting

Once we have the predicted model of any structural element included in our map, to fit that model in the volume constitutes the next step in the modeling workflow. Two protocols have been included in Scipion with this purpose, phenix-dock in map (Appendix PHENIX Dock in map [Liebschner et al., 2019]) and chimerax-rigid fit (Appendix CHIMERAX Rigid fit). The first one allows automatic fitting of models in maps, while the second one only does it when model and map are quite close, thus requiring manual fitting in advance. Although there is no a general rule to fit map and model, because it will depend on the particular problem and on our previous knowledge, in this tutorial we are going to use phenix-dock in map application first, followed by the final Fit in map in chimerax-rigid fit. Observe these two new steps in the modeling Scipion workflow in Fig. 10.1.

Fig. 10.1 Scipion framework detailing the workflow to fit the first model of the human Hgb \alpha subunit in the map asymmetric unit.

10.1. Initial rigid fit with PHENIX dock in map

Open phenix-dock in map protocol (Fig. 10.2 (1)), and complete the form with the the extracted map asymmetric unit (2), the map resolution (3), the model of atomic structure previously saved in ChimeraX (4), and the number of copies of this atomic structure that we’d like to fit in the map, 1 in this case (5). As an additional exercise you can check the result of fitting two copies of this structure in the initial input map.

Fig. 10.2 Rigid fit with phenix-dock in map protocol: Filling in the protocol form.

After executing the protocol phenix-dock in map (Fig. 10.2 (6)), you can check the docking results clicking in Analyze Results (7). ChimeraX graphics window will be opened (Fig. 10.3) showing the map and the atomic structure modeled in its initial location (pink) and fitted in the map (green) (Fig. 10.3 (1)).

Fig. 10.3 Rigid fit with phenix-dock in map: View of docking results in ChimeraX.

A rough inspection of the placed_model in Fig. 10.3 (remark the location of the HEME group, for example, which should be moved slightly to the right side) shows that the fitting could be improved a little. The second protocol, chimerax-rigid fit, will help in this purpose.

10.2. Completing rigid fit with CHIMERAX rigid fit

Important

before starting!!! As we already advised previously, we are going to use a ChimeraX-derived protocol (chimerax-rigid fit, Appendix CHIMERA Rigid fit). Remark that this use of ChimeraX is completely different from the use of ChimeraX as a visualization tool. By using the ChimeraX graphics window, opening it from the Scipion button Analyze Results, we can observe protocol results but we CANNOT save anything in Scipion. However, using ChimeraX as a tool, as it is the case in Scipion ChimeraX-derived protocols, we can perform different tasks, taking advantage of the available ChimeraX tools and, finally, we CAN save the obtained results and the working session in Scipion.

To complete the rigid fitting of the model generated in the previous step, open the protocol chimerax-rigid fit, include again the map of the asymmetrical unit (2), and the just fitted model of the human metHgb \alpha subunit (3), and execute the protocol (4).

Fig. 10.4 Completing the ChimeraX rigid fit protocol form.

Once opened the ChimeraX graphical window, we can complete the fitting of the model to the map, by command line or through the ChimeraX GUI.

• By ChimeraX command line, considering that map and model have ID numbers #2 and #3 (Fig. 10.5 (B)):

fitmap #3 inMap #2

• By the ChimeraX GUI: Select in the upper main menu Tools -> Volume Data -> Fit in Map. A small window will be opened (Fig. 10.5 (A)). Select the appropriate model to fit in the map and press Fit (1) to allow the automatic rigid fitting.

A slight movement to the right perfectly fits map and model, as can be observed in (Fig. 10.5 (B)). To facilitate the visual inspection of the fitting we can replace the surface view of the map by mesh as indicated in (A). Observe this time the right placement of the HEME group in the map density.

To use the side view as additional tool to observe the fit, select in the upper main menu Tools -> General -> Side View.

Fig. 10.5 Fit in map with ChimeraX.

To track the ChimeraX fitted model in Scipion we have to save it as fitted model of the metHgb \alpha subunit in the ChimeraX command line before closing the ChimeraX window:

scipionwrite #3 prefix Hgb_alpha_
exit

The string that we have included as prefix in the command line will allow us to follow the atomic structure in a more simple manner. In particular, if you click Analyze Results (Fig. 10.4 (6)) the ChimeraX graphics window will open again and you can check the prefix in the the name of the saved atomic structure (Hgb_alpha_Atom_struct_3_003753) in the Models panel of Fig. 10.6 (1). Interestingly, the suffix number of the saved atomic structure (003753) stands for the ID protocol number and you can check it by simply surfing the mouse over the protocol (Fig. 10.4 (5)).

Fig. 10.6 View in ChimeraX graphics window of the initial model of human Hgb \alpha subunit fitted to the asymmetrical unit of the 3D map.