Aligning reconstructions with high resolution shapes ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ It is often important to align SAXS reconstructions, either bead models such as those from DAMMIF/N or electron density from DENSS, with high resolution structural models such as those from x-ray crystallography to see how well they agree. RAW can do that automatically when you generate the models, as described in the :ref:`DAMMIF/N ` and :ref:`DENSS ` sections of the tutorial. RAW also provides standalone windows for doing the alignment with already generated reconstructions. A video version of this tutorial is available: .. raw:: html
The written version of the tutorial follows. Bead models - SUPCOMB ************************* .. _raw_supcomb: SUPCOMB from the ATSAS suite can be used to align two PDB files. In this context, one model (the reference) is the high resolution structure while the other (the target) is the bead model reconstruction. #. Open the SUPCOMB window by selecting Tools->ATSAS->SUPCOMB from the menu bar |align_supcomb_menu_png| #. In the window that opens, 'Target' is the model that is aligned, where as 'Reference' is the model that the target is aligned to. In other words, the Reference model stays unchanged, while the Target model is moved to best align with the Reference. #. Use the Reference 'Select' button to select **reconstruction_data/gi_complete/1XIB_4mer.pdb** as the reference file. * *Tip:* Only the filename will show up in either the Reference or Target box. If you hover your mouse over the filename it will show the full path to the file. #. Use the Target 'Select' button to select **reconstruction_data/gi_complete/gi_dammif/refine_glucose_isomerase-1.pdb** |align_supcomb_select_png| #. Click the start button. SUPCOMB will run. |align_supcomb_start_png| #. When SUPCOMB is finished, in the same folder as the target file you will see a **_aligned.pdb** file, which is the target model aligned with the reference file. #. Advanced settings can be accessed by clicking on the 'Advanced Settings' text to expand the section. These settings are described in the `SUPCOMB manual `_. |align_supcomb_advanced_png| Electron density ************************* DENSS include a native tool for aligning two electron density files (.mrc) or an electron density to a PDB file. In this context, one model (the reference) is the high resolution #. Open the Electron Density Alignment window by selecting Tools->Electron Density (DENSS) Alignment from the menu bar |align_denss_menu_png| #. In the window that opens, 'Target' is the model that is aligned, where as 'Reference' is the model that the target is aligned to. In other words, the Reference model stays unchanged, while the Target model is moved to best align with the Reference. #. Use the Reference 'Select' button to select **reconstruction_data/gi_complete/1XIB_4mer.pdb** as the reference file. * *Tip:* Only the filename will show up in either the Reference or Target box. If you hover your mouse over the filename it will show the full path to the file. #. Use the Target 'Select' button to select **reconstruction_data/gi_complete/gi_denss/glucose_isomerase_refine.mrc** |align_denss_select_png| #. Click the start button. DENSS alignement will run. * *Tip:* If there is already a file in the folder with the aligned output filename you will get a prompt to overwrite it. * *Tip:* By default, DENSS centers the Reference file. This writes out a file namged **_centered.pdb** in the same folder as the reference file, which is what should be compared to the aligned file. You can turn this off in the Advanced Settings. |align_denss_start_png| #. When alignment is finished, in the same folder as the target file you will see a **_aligned.mrc**. Compare this to the **_centered.pdb** file in reference file folder. In this case those names are **glucose_isomerase_refine_aligned.mrc** and **1XIB_4mer_centered.pdb**. #. You can change the advanced settings by expanding the Advanced Settings section. These advanced settings are: * *Number of cores:* Number of cores to use during alignment * *Enantiomorphs:* Whether to generate enantiomorphs of the Target before doing the alignment. * *Center reference:* Whether to center the reference model at the origin. If used, this creates a **_centered.pdb** file in the same folder as the reference file. * *PDB calc. resolution:* The resolution of the density map created from the Reference PDB model to compare with the Target model. This has no effect if the Reference is already a density. |align_denss_advanced_png| .. |align_supcomb_menu_png| image:: images/align_supcomb_menu.png :width: 400 px :target: ../_images/align_supcomb_menu.png .. |align_supcomb_select_png| image:: images/align_supcomb_select.png :width: 400 px :target: ../_images/align_supcomb_select.png .. |align_supcomb_start_png| image:: images/align_supcomb_start.png :width: 400 px :target: ../_images/align_supcomb_start.png .. |align_supcomb_advanced_png| image:: images/align_supcomb_advanced.png :width: 400 px :target: ../_images/align_supcomb_advanced.png .. |align_denss_menu_png| image:: images/align_denss_menu.png :width: 250 px :target: ../_images/align_denss_menu.png .. |align_denss_select_png| image:: images/align_denss_select.png :width: 400 px :target: ../_images/align_denss_select.png .. |align_denss_start_png| image:: images/align_denss_start.png :width: 400 px :target: ../_images/align_denss_start.png .. |align_denss_advanced_png| image:: images/align_denss_advanced.png :width: 400 px :target: ../_images/align_denss_advanced.png