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auto3dem:documentation:protocols:asymmetric_reconstruction [2015/04/14 14:08] gcardone created |
auto3dem:documentation:protocols:asymmetric_reconstruction [2015/04/15 10:51] (current) gcardone |
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| * **Generate a suitable template**\\ Generate a reference map containing additional density, placed at just one equivalent site where the component is expected. The density can be generated synthetically, or by merging the icosahedral reconstruction with the density from some available reconstruction of the component. Generally it does not need to be a faithful representation of such component. | * **Generate a suitable template**\\ Generate a reference map containing additional density, placed at just one equivalent site where the component is expected. The density can be generated synthetically, or by merging the icosahedral reconstruction with the density from some available reconstruction of the component. Generally it does not need to be a faithful representation of such component. | ||
| * **Modify the parameter file**\\ Modify the last parameter file generated by Auto3DEM (file ending with _continue), possibly saving it with a different name for bookkeeping purposes. | * **Modify the parameter file**\\ Modify the last parameter file generated by Auto3DEM (file ending with _continue), possibly saving it with a different name for bookkeeping purposes. | ||
| - | * change the reference map by pointing the following parameters to the asymmetric template\\ auto start_map\\ auto start_map_even\\ auto start_map_odd | + | * change the reference map by pointing the following parameters to the asymmetric template\\ ''auto start_map''\\ ''auto start_map_even''\\ ''auto start_map_odd'' |
| - | * release the constraint of icosahedral symmetry by deleting the line\\ auto symm_code 532 | + | * release the constraint of icosahedral symmetry by deleting the line\\ ''auto symm_code 53''2 |
| - | * don't apply any radial mask\\ auto hollow_map 0\\ Alternatively you can set an optimal radial range by keeping the parameter set to 1, and setting manually the values of\\ auto hollow_in_rad\\ auto hollow_out_rad\\ to include all the asymmetric reconstruction, after making sure that\\ auto hollow_auto 0 | + | * don't apply any radial mask\\ ''auto hollow_map 0''\\ Alternatively you can set an optimal radial range by keeping the parameter set to 1, and setting manually the values of\\ ''auto hollow_in_rad''\\ ''auto hollow_out_rad''\\ to include all the asymmetric reconstruction, after making sure that\\ ''auto hollow_auto 0'' |
| - | * avoid solvent flattening of the map to assure that the asymmetric feature is fully included in the reference\\ auto flatten_map 0 | + | * avoid solvent flattening of the map to assure that the asymmetric feature is fully included in the reference\\ ''auto flatten_map 0'' |
| - | * set the refinement to search only among the 60 solutions equivalent to the one previously determined\\ po2r mode ticos_equiv | + | * set the refinement to search only among the 60 solutions equivalent to the one previously determined\\ ''po2r mode ticos_equiv'' |
| - | * fix the center coordinates of the particles to reduce the risk of bias\\ po2r ncenter 0 | + | * fix the center coordinates of the particles to reduce the risk of bias\\ ''po2r ncenter 0'' |
| - | * use only low resolution features to determine the best orientation\\ po2r res_max 40\\ The value of 40 Å is just indicative, although a good start, and can be changed to reflect the size of the asymmetric component. | + | * use only low resolution features to determine the best orientation\\ ''po2r res_max 40''\\ The value of 40 Å is just indicative, although a good start, and can be changed to reflect the size of the asymmetric component. |
| - | * keep the resolution range constant from one iteration to the next\\ auto freeze_res 1 | + | * keep the resolution range constant from one iteration to the next\\ ''auto freeze_res 1'' |
| - | * generate a reconstruction, after the refinement, without imposing any symmetry\\ p3dr symm_code 1 | + | * generate a reconstruction, after the refinement, without imposing any symmetry\\ ''p3dr symm_code 1'' |
| * **Generate an initial asymmetric map**\\ Using the modified parameter file, run 3 to 5 iterations, until the reconstruction does not change. | * **Generate an initial asymmetric map**\\ Using the modified parameter file, run 3 to 5 iterations, until the reconstruction does not change. | ||
| - | * **Refine the reconstruction**\\ Run additional iterations after modifying the last parameter file generated by Auto3DEM by changing back few parameters\\ auto freeze_res 0\\ po2r mode local\\ po2r ncenter 4\\ auto flatten_map 1 (optional)\\ Additionally, set\\ auto res_max\\ to a resolution value close but larger than the resolution estimated by the program for the latest asymmetric reconstruction. | + | * **Refine the reconstruction**\\ Run additional iterations after modifying the last parameter file generated by Auto3DEM by changing back few parameters\\ ''auto freeze_res 0''\\ ''po2r mode local''\\ ''po2r symm_code 1''\\ ''po2r ncenter 4''\\ ''auto flatten_map 1'' (optional)\\ Additionally, set\\ ''auto res_max''\\ to a resolution value close but larger than the resolution estimated by the program for the latest asymmetric reconstruction. |