.. _`compareInitialModel`: Comparison of ModelAngelo generated models with the published traced atomic structure ===================================================================================== In this section we are going to overlap the TACAN ModelAngelo derived structure with the structure already published and traced (`PDB 7F3U `_) to interpret the same map (`EMD-31441 `_). Two different protocols can be used to overlap and visualize structures, **chimerax-operate** (Appendix :ref:`CHIMERA Operate `), and **phenix-superpose pdbs** (Appendix :ref:`PHENIX Superpose PDBs `). Using these protocols we will cover steps 6, 7 and 8 of the general workflow (:numref:`model_building_modelangelo_fig1_workflow`), although the previous and common step 5 is required to import the atomic structure 7F3U. To import in *Scipion* the atomic structure, open the protocol **import atomic structure** (Appendix :ref:`Import atomic structure `) and complete the form including the PDB ID as indicated in :numref:`model_building_modelangelo_import_structure` (1). .. figure:: Images/Fig9_import_structure.svg :alt: Completing protocol **import atomic structure** with PDB ID (workflow step 5; :numref:`model_building_modelangelo_fig1_workflow`). :name: model_building_modelangelo_import_structure :align: center :width: 100.0% Completing protocol **import atomic structure** with PDB ID (workflow step 5; :numref:`model_building_modelangelo_fig1_workflow`). Overlapping models in *ChimeraX* -------------------------------- Open the protocol **chimerax-operate** (Appendix :ref:`CHIMERA Operate `) and fill in the form as indicated in :numref:`model_building_modelangelo_operate_1`. Complete the form with the atomic structure recently downloaded in *Scipion* (1) and a structure generated with ModelAngelo (2). In this case we have selected the pruned one obtained in step 3 of the general workflow (:numref:`model_building_modelangelo_fig1_workflow`). Then execute the protocol. .. figure:: Images/Fig10_chimerax_operate_1.svg :alt: Filling in the Scipion protocol **chimerax-operate** (workflow steps 6 and 7; :numref:`model_building_modelangelo_fig1_workflow`). :name: model_building_modelangelo_operate_1 :align: center :width: 100.0% Filling in the Scipion protocol **chimerax-operate** (workflow steps 6 and 7; :numref:`model_building_modelangelo_fig1_workflow`). *ChimeraX* :cite:p:`Goddard2018` GUI will open to show both atomic structures overlapped as shown in :numref:`model_building_modelangelo_operate_2`, C. .. figure:: Images/Fig11_chimerax_operate_results_1.svg :alt: Atomic structures from PDB ID 7F3U (**A**), pruned ModelAngelo generated model in :numref:`model_building_modelangelo_results_1` (F) (**B**), and both models overlapped (**C**). :name: model_building_modelangelo_operate_2 :align: center :width: 100.0% Atomic structures from PDB ID 7F3U (**A**), pruned ModelAngelo generated model in :numref:`model_building_modelangelo_results_1` (F) (**B**), and both models overlapped (**C**). *ChimeraX* models #2 and #3 are the publised structure 7F3U and the pruned model generated by ModelAngelo, respectively. First, we can color model #3 according to the values of the B-factor column using *AlphaFold* criteria writing in *ChimeraX* command line: :: color bfactor #3 palette alphafold Although both structures are quite close, a perfect matching can be obtained writing in *ChimeraX* command line: :: mmaker #3 to #2 `mmaker `_ superimposes proteins or nuceic acids by fitting aligned residue pairs using one atom per residue. Then, model #3, sligthly moved to fit to model #2, can be saved in *Scipion* with the *ChimeraX* command line: :: scipionwrite #3 prefix modelangelo_structure_ With this superposition of structures we can inspect similarities and differences between the previously traced structure and the one predicted by ModelAngelo, in a similar way as we have done in :numref:`model_building_modelangelo_results_4`. Overlapping models in *Phenix* ------------------------------ **phenix-superpose pdbs** protocol (Appendix :ref:`PHENIX Superpose PDBs `) also allows superposing atomic structures using the *Phenix* function `superpose_pdbs `_. Open the protocol **phenix-superpose pdbs** and fill in the form as indicated in :numref:`model_building_modelangelo_superpose`. Complete the form with the atomic structure recently downloaded in *Scipion* (1) and a structure generated with ModelAngelo (2). In this case we have selected the pruned one obtained in step 3 of the general workflow (:numref:`model_building_modelangelo_fig1_workflow`). Remark that in this case the first structure will remain fixed and only the second one will move to fit to the first one. Then execute the protocol. .. figure:: Images/Fig12_phenix_superpose_pdbs.svg :alt: Filling in the *Scipion* protocol **phenix-superpose pdbs** (workflow step 8; :numref:`model_building_modelangelo_fig1_workflow`). :name: model_building_modelangelo_superpose :align: center :width: 95.0% Filling in the *Scipion* protocol **phenix-superpose pdbs** (workflow step 8; :numref:`model_building_modelangelo_fig1_workflow`). After executing the protocol, output result can be visualized clicking **Analyze Results**. *ChimeraX* viewer will open and three overlapping models can be observed (:numref:`model_building_modelangelo_superpose_results`, A, E): The published atomic structure `7F3U `_, in blue, the pruned ModelAngelo generated structure, in purple, and the protocol output superposed structure, in orange. .. figure:: Images/Fig13_phenix_superpose_results.svg :alt: Output result from *Scipion* protocol **phenix-superpose pdbs**. **A**: Overlapped models 7F3U, pruned ModelAngelo prediction and superposed struture. **B**: Overlapped models pruned ModelAngelo prediction and superposed struture. **C**: Pruned ModelAngelo prediction. **D**: Ouput protocol superpose model. **E**: *ChimeraX* Models panels. **F**: Protocol summary detailing RMSD between fixed and moving atoms. :name: model_building_modelangelo_superpose_results :align: center :width: 100.0% Output result from *Scipion* protocol **phenix-superpose pdbs**. **A**: Overlapped models 7F3U, pruned ModelAngelo prediction and superposed struture. **B**: Overlapped models pruned ModelAngelo prediction and superposed struture. **C**: Pruned ModelAngelo prediction. **D**: Ouput protocol superpose model. **E**: *ChimeraX* Models panels. **F**: Protocol summary detailing RMSD between fixed and moving atoms. Comparing the input pruned ModelAngelo prediction model and the output superposed one (:numref:`model_building_modelangelo_superpose_results`, C, D) we can observe that the superposed structure has been rotated 180 degrees regarding a vertical axis to get a fitting involving a higher number of residues. The correlation improvement is detailed also in the protocol Summary (:numref:`model_building_modelangelo_superpose_results`, F).