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auto3dem:documentation:protocols:gold_standard [2015/04/14 15:32]
gcardone created
auto3dem:documentation:protocols:gold_standard [2015/07/08 11:09] (current)
gcardone [Limitations]
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 generate the //.date// and //.dato// files on his/her own, since autopp only generate the //.date// and //.dato// files on his/her own, since autopp only
 splits by sequential numbering. ​ splits by sequential numbering. ​
-<WRAP center round info 85%> 
-If you use the Random Model method implemented in Auto3DEM to generate an ab-initio reference map, the program takes care to generate the two independent stack parameter files, along with a _master file set for the gold standard procedure.</​WRAP>​ 
  
 ===== Reference maps ===== ===== Reference maps =====
 +Each half set of particles needs to be aligned against a different reference.
 In the parameter file controlling the workflow of Auto3DEM (usually In the parameter file controlling the workflow of Auto3DEM (usually
-ending with _master or _continue) ​there is a new flag in the control +ending with _master or _continue) the reference maps for the two independent sets are specified in 
-parameters, that is 'auto gold_standard',​ which is set to 1 by default. +the fields 
-Also, the reference maps for the two independent sets are specified in +  ​auto  start_map_even 
-the fields ​'auto  start_map_even' and  'auto start_map_odd'. In order to +  ​auto ​ start_map_odd 
-succesfully run the procedure, ​an additional constraint ​is required: ​+When starting ​the iterative ​procedure, ​the same map can be used as initial reference for both the two sets, as long as only the low resolution features are used determining the alignment parameters. This is achieved by setting either the parameter ''​ppft resolution_high''​ or ''​po2r res_max'',​ depending if ''​auto mode''​ is set to ''​search''​ or ''​refine'',​ respectively,​ to 30 Å or higher.
  
-As result ​of the procedure, after each iteration three maps are +===== Aligning the particles ===== 
-actually generated: one from each set and one from all the particles. +In the parameter file controlling the workflow of Auto3DEM ​flag, ''​auto gold_standard'',​ controls the use of the gold standard procedure. If set to 1, the fields ''​data''​ can only contain a list of stack parameter files properly split, that is only //.dato// and //.date// files are accepted. If the flag is set to 0, no gold standard procedure is followed, all the stack parameter files are treated as one single data set, and their particles are aligned against the map listed in the parameter ''​auto start_map''​. 
-The last one is just for visualization purposes, and only its radial +In the gold standard ​procedure, after each iteration three maps are actually generated: one from each set and one from all the particles. The last one is just for visualization purposes, and only its radial amplitude profile is utilized to re-calibrate some masking parameters. 
-amplitude profile is utilized to re-calibrate some masking parameters.+ 
 +<WRAP center round info 85%> 
 +If you use the Random Model method implemented in Auto3DEM to generate an ab-initio reference map, the program takes care to generate the two independent stack parameter files, along with a _master file properly set for the gold standard procedure.</​WRAP>​
  
 +===== Limitations =====
 Currently there are two caveats in the procedure: Currently there are two caveats in the procedure:
 <WRAP center round important 85%> <WRAP center round important 85%>
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 and if the handedness is different then: and if the handedness is different then:
   - modify the stack parameter files from the last iteration, for only one set, using the command //​handflip//;​   - 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 bsoftwith 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 mapgo to the menu ''​Manipulate/​Invert 3D Map'',​ select ''​Reflect in xy plane (z -> -z)'', and save the modified map).
 </​WRAP>​ </​WRAP>​
-