pipeline:cter:sxgui_cter

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pipeline:cter:sxgui_cter [2019/06/07 13:49]
shaikh [Typical usage]
pipeline:cter:sxgui_cter [2019/09/12 18:49] (current)
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.
  
  • pipeline/cter/sxgui_cter.1559908165.txt.gz
  • Last modified: 2019/06/07 13:49
  • by shaikh