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pipeline:cter:sxgui_cter [2019/06/07 13:46]
shaikh [Typical usage] 		pipeline:cter:sxgui_cter [2019/09/12 18:49]
shaikh
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 ===== Typical usage ===== ===== Typical usage =====
  
-sp_gui_cter GUI tool can be run as a stand-alone program or run from the SPHIRE GUI.+Standard usage: sp_gui_cter can be run as a stand-alone program or run from the SPHIRE GUI:
  
-  sp_gui_cter.py  outdir_cter/partres.txt+  sp_gui_cter.py  CTER_DIR/partres.txt
  
 Upon startup, the following windows will appear: Upon startup, the following windows will appear:
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   ; Histogram : Plot of number of micrographs as a function of a selected parameter (see below)   ; Histogram : Plot of number of micrographs as a function of a selected parameter (see below)
   ; Sort Plot : Plot of a selected parameter (see below) for each micrograph   ; Sort Plot : Plot of a selected parameter (see below) for each micrograph
 +[{{ :pipeline:cter:cter_mic0007.png?600 |Main CTER window (top left) with "Sync. w/sort" activated", Rotational average plot, zoomed (top right), Sort plot (bottom left), histogram (bottom right)}}]
  
 The following windows are not displayed by default, to minimize the number of pop-up windows, and can be displayed by clicking on the corresponding checkbox from the Control Panel window, under Display Windows at the top left.  The following windows are not displayed by default, to minimize the number of pop-up windows, and can be displayed by clicking on the corresponding checkbox from the Control Panel window, under Display Windows at the top left. 
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   ; Micrograph Thumbnail : Downsampled (512x512) micrograph   ; Micrograph Thumbnail : Downsampled (512x512) micrograph
   ; 2D Power Spectrum : Periodogram of micrograph, with one quarter replaced by the theoretical form. Circle is drawn at the astigmatism resolution limit.   ; 2D Power Spectrum : Periodogram of micrograph, with one quarter replaced by the theoretical form. Circle is drawn at the astigmatism resolution limit.
 +[{{ :pipeline:cter:cter_pws0007.png?600 |2D power spectrum (left), with theoretical spectrum in top right; micrograph thumbnail (right)}}]
 +
 +sp_gui_cter can also be used to visualize CTFFIND output.
 +
 +  sp_gui_cter.py  CTFFIND_DIR/partres.txt --ctffind
      
 +TranSPHIRE generates compatible partres files. 
 +Note, however, that TranSPHIRE does not currently write 2D power spectra to a single directory, nor does CTFFIND write micrograph thumbnails.
 +If you wish to visualize these outputs, move them to respective subdirectories, and specify them:
 +
 +If these files are not present, the program will simply display a warning, and you can continue.
 +
 +[{{ :pipeline:cter:ctffind.png?600 |}}]
 +
 The parameter that will be plotted on the Histogram and Sort Plot is selected under Histogram & Plot Settings. The default parameter is defocus. Micrographs in the Sort Plot and micrograph list are initially sorted by micrograph number (or the order in which they appear in the partres file, i.e., CTER ID). By clicking Sync w/Sort, the micrographs will be sorted from low to high defocus. Micrographs in the Sort Plot and micrograph list can be sorted by the parameter selected under the pulldown menu Sort CTER Partres Entries. The parameter that will be plotted on the Histogram and Sort Plot is selected under Histogram & Plot Settings. The default parameter is defocus. Micrographs in the Sort Plot and micrograph list are initially sorted by micrograph number (or the order in which they appear in the partres file, i.e., CTER ID). By clicking Sync w/Sort, the micrographs will be sorted from low to high defocus. Micrographs in the Sort Plot and micrograph list can be sorted by the parameter selected under the pulldown menu Sort CTER Partres Entries.
  
 Outliers in the parameter selected in Histogram & Plot Settings can be removed in three ways: Outliers in the parameter selected in Histogram & Plot Settings can be removed in three ways:
  
-  ; 1. Thresholds can be dragged on the Histogram or Sort Plot. The lower limit is displayed as a blue dotted line, and the upper limit in red. Clicking on either plot will set the lower limit to this value. To set the upper limit, go to the pulldown menu Move Threshold, and select Upper (red).  +  ; 1. Histogram or Sort Plot : Thresholds can be dragged on the Histogram or Sort Plot. The lower limit is displayed as a blue dotted line, and the upper limit in red. Clicking on either plot will set the lower limit to this value. To set the upper limit, go to the pulldown menu Move Threshold, and select Upper (red).  
-  ; 2. In the table of parameters labeled Unapplied Thresholds, edit the value for the selected parameter. Initially, only the limit selected under the Move Threshold pulldown menu will be editable. To edit both the lower and upper limit, select Edit only under the Move Threshold pulldown. +  ; 2. Edit Unapplied Thresholds : In the table of parameters labeled Unapplied Thresholds, edit the value for the selected parameter. Initially, only the limit selected under the Move Threshold pulldown menu will be editable. To edit both the lower and upper limit, select Edit only under the Move Threshold pulldown. 
-  ; 3. Load previously set thresholds, if available, by clicking Load and selecting the threshold text file of the form Trial00_thresholds.txt. To see how to create such a file, see below.+  ; 3. Load Thresholds file : Load previously set thresholds, if available, by clicking Load and selecting the threshold text file of the form Trial00_thresholds.txt. To see how to create such a file, see below.
      
 In addition to defocus value, another potentially useful metric to sort is Astigmatism Frequency Limit. This number tells us to what resolution CTER was able to fit the experimental power spectrum, when taking astigmatism into account. Micrographs with a poor resolution limit may not be useful for obtaining a high-resolution reconstruction. In addition to defocus value, another potentially useful metric to sort is Astigmatism Frequency Limit. This number tells us to what resolution CTER was able to fit the experimental power spectrum, when taking astigmatism into account. Micrographs with a poor resolution limit may not be useful for obtaining a high-resolution reconstruction.
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 Clicking on Save Selection will write out the following files: Clicking on Save Selection will write out the following files:
  
-  ; Trial00_micrographs_select.txt : List of selected micrographs +  ; Trial00_micrographs_ select.txt : List of selected micrographs 
-  ; Trial00_micrographs_discard.txt : List of selected micrographs +  ; Trial00_micrographs_ discard.txt : List of selected micrographs 
-  ; Trial00_partres_select.txt: CTF parameters of the selected micrographs +  ; Trial00_partres_ select.txt : CTF parameters of the selected micrographs 
-  ; Trial00_partres_discard.txt: CTF parameters of the deselected micrographs +  ; Trial00_partres_ discard.txt : CTF parameters of the deselected micrographs 
-  ; Trial00_thresholds.txt: Applied thresholds for each parameter+  ; Trial00_thresholds.txt : Applied thresholds for each parameter
      
 The default prefix for output files can be changed from Trial00 by changing the value in the field File Suffix. (Note: should be Prefix) The default prefix for output files can be changed from Trial00 by changing the value in the field File Suffix. (Note: should be Prefix)
pipeline/cter/sxgui_cter.txt · Last modified: 2019/09/12 18:49 by shaikh

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