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auto3dem:documentation:protocols:gold_standard [2015/04/14 17:10] gcardone [Limitations] |
auto3dem:documentation:protocols:gold_standard [2015/07/08 11:09] (current) gcardone [Limitations] |
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| - change the handedness of the corresponding reconstruction. This can be done either by recomputing the reconstruction from the modified parameter files (open the last _continue file, set ''auto generate_map only'', save it and run it), or by modifying the map using Robem (open the map, go to the menu ''Manipulate/Invert 3D Map'', select ''Reflect in xy plane (z -> -z)'', and save the modified map). | - change the handedness of the corresponding reconstruction. This can be done either by recomputing the reconstruction from the modified parameter files (open the last _continue file, set ''auto generate_map only'', save it and run it), or by modifying the map using Robem (open the map, go to the menu ''Manipulate/Invert 3D Map'', select ''Reflect in xy plane (z -> -z)'', and save the modified map). | ||
| </WRAP> | </WRAP> | ||
| - | <WRAP center round important 85%> | ||
| - | **Background masking**\\ | ||
| - | Currently the two independent reference maps generated at each iteration are not low-pass filtered, and therefore the level of noise from the high frequency regions is very high. For this reason the option to perform a //solvent flattening// of these maps, when used as references, is not successful, since the algorithm can not discriminate between density and noise. Therefore, when using the gold standard procedure the flattening option must be avoided by setting | ||
| - | auto flatten_map 0 | ||
| - | </WRAP> | ||
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