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--- auto3dem:documentation:protocols:gold_standard [2015/04/14 16:49]
gcardone
+++ auto3dem:documentation:protocols:gold_standard [2015/07/08 11:09]
gcardone [Limitations]
@@ Line 61: / Line 61: @@
 and if the handedness is different then:
   - modify the stack parameter files from the last iteration, for only one set, using the command //handflip//;
-  - change the handedness of the corresponding reconstruction. This can be done either recomputing the reconstruction from the modified parameter files (in the last  _continue file, just set 'auto generate_map' to 'only' and launch it), or by modifying the map using an external program (e.g. using the program //bimg// from bsoft, with the option '-reslice xy-z').
+  - 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 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>