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 :ref:`PHENIX Dock in map ` :cite:p:`Liebschner2019`) and **chimerax-rigid fit** (Appendix :ref:`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 :numref:`model_building_scipion_workflow_rigidfit`. .. figure:: Images/Fig67.svg :alt: *Scipion* framework detailing the workflow to fit the first model of the human *Hgb* :math:`\alpha` subunit in the map asymmetric unit. :name: model_building_scipion_workflow_rigidfit :align: center :width: 100.0% *Scipion* framework detailing the workflow to fit the first model of the human *Hgb* :math:`\alpha` subunit in the map asymmetric unit. Initial rigid fit with *PHENIX dock in map* ------------------------------------------- Open **phenix-dock in map** protocol (:numref:`model_building_dockInMap_protocol` (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. .. figure:: Images/Fig18.svg :alt: Rigid fit with **phenix-dock in map** protocol: Filling in the protocol form. :name: model_building_dockInMap_protocol :align: center :width: 100.0% Rigid fit with **phenix-dock in map** protocol: Filling in the protocol form. After executing the protocol **phenix-dock in map** (:numref:`model_building_dockInMap_protocol` (6)), you can check the docking results clicking in *Analyze Results* (7). *ChimeraX* graphics window will be opened (:numref:`model_building_dockInMap_results`) showing the map and the atomic structure *modeled* in its initial location (pink) and fitted in the map (green) (:numref:`model_building_dockInMap_results` (1)). .. figure:: Images/Fig20.svg :alt: Rigid fit with **phenix-dock in map**: View of docking results in *ChimeraX*. :name: model_building_dockInMap_results :align: center :width: 85.0% Rigid fit with **phenix-dock in map**: View of docking results in *ChimeraX*. A rough inspection of the *placed_model* in :numref:`model_building_dockInMap_results` (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. 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 :ref:`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* :math:`\alpha` subunit (3), and execute the protocol (4). .. figure:: Images/Fig21.svg :alt: Completing the *ChimeraX* rigid fit protocol form. :name: model_building_chimera_rigid_fit :align: center :width: 100.0% 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* (:numref:`model_building_chimera_fit_in_map` (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 (:numref:`model_building_chimera_fit_in_map` (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 (:numref:`model_building_chimera_fit_in_map` (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*. .. figure:: Images/Fig22.svg :alt: Fit in map with *ChimeraX*. :name: model_building_chimera_fit_in_map :align: center :width: 85.0% Fit in map with *ChimeraX*. | To track the *ChimeraX* fitted *model* in *Scipion* we have to save it as fitted *model* of the *metHgb* :math:`\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* (:numref:`model_building_chimera_rigid_fit` (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 :numref:`model_building_chimera_fit_results_2` (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 (:numref:`model_building_chimera_rigid_fit` (5)). .. figure:: Images/Fig23.svg :alt: View in *ChimeraX* graphics window of the initial *model* of human *Hgb* :math:`\alpha` subunit fitted to the asymmetrical unit of the 3D map. :name: model_building_chimera_fit_results_2 :align: center :width: 85.0% View in *ChimeraX* graphics window of the initial *model* of human *Hgb* :math:`\alpha` subunit fitted to the asymmetrical unit of the 3D map.