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pipeline:subtract:avgfilt [2021/02/01 15:23]
shaikh 		pipeline:subtract:avgfilt [2021/02/12 11:32] (current)
shaikh [Reference]
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 Choose a low-pass filter radius so that a permissive (i.e., low) surface threshold can be used in Chimera.  If too high a threshold is used during segmentation, then the resulting mask may not encapsulate the entire region of interest.  If a low threshold is used on a not-post-processed high-resolution map, then disconnected "moon" densities will be included in the segmentation. Choose a low-pass filter radius so that a permissive (i.e., low) surface threshold can be used in Chimera.  If too high a threshold is used during segmentation, then the resulting mask may not encapsulate the entire region of interest.  If a low threshold is used on a not-post-processed high-resolution map, then disconnected "moon" densities will be included in the segmentation.
 +
 +[{{:pipeline:subtract:2-segmented.png?410 |Segmented map after low-pass filtration}}][{{ :pipeline:subtract:unfil-segmented.png?410|Segmented map without low-pass filtration}}]
      
 Note 1: If you already have an averaged map, or don't have two maps to average, skip the '--avol2' flag. Note 1: If you already have an averaged map, or don't have two maps to average, skip the '--avol2' flag.
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 \\ __2. Locate regions to be subtracted __ \\ __2. Locate regions to be subtracted __
  
-\\ __3. Mask a soft mask of the region to be excluded __+\\ __3. [[sp_mask|Mask a soft mask of the region to be excluded]] __
  
-\\ __4. Compute re-projections of map to be subtracted, and subtract them from the original images __+\\ __4. [[projsubtract|Compute re-projections of map to be subtracted, and subtract them from the original images]] __
  
-\\ __5. Compute reconstruction of density remaining after signal-subtraction __+\\ __5. [[pipeline:meridien:sxmeridien|Compute reconstruction of density remaining after signal-subtraction]] __
  
-\\ __6. Center map of the remaining density __+\\ __6. [[centershift|Center map of the remaining density]] __
  
 \\ \\
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   ; vol_avg_fil.hdf : Low-pass filtered average of input half-set maps.   ; vol_avg_fil.hdf : Low-pass filtered average of input half-set maps.
   ; input_filtered.hdf : Low-pass filtered input map.   ; input_filtered.hdf : Low-pass filtered input map.
- +[{{ :pipeline:subtract:1-filtered.png?410 | Unfiltered map (yellow), low-pass filtered map (transparent cyan)}}] 
 \\ \\
 ===== Description ===== ===== Description =====
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 \\ \\
 ==== Reference ==== ==== Reference ====
 +Bai XC, Yan C, Yang G, Lu P, Ma D, Sun L, Zhou R, Scheres SHW, Shi Y. (2015) "An atomic structure of human γ-secretase." //Nature// **525**: 212-217. doi: 10.1038/nature14892.
 \\ \\
 ==== Developer Notes ==== ==== Developer Notes ====
pipeline/subtract/avgfilt.1612189392.txt.gz · Last modified: 2021/02/01 15:23 by shaikh

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