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pipeline:cter:sxgui_cter [2019/06/07 13:48] 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 | + | Standard usage: |
- | sp_gui_cter.py | + | sp_gui_cter.py |
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 | ||
+ | [{{ : | ||
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. | ||
+ | [{{ : | ||
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+ | sp_gui_cter can also be used to visualize CTFFIND output. | ||
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+ | sp_gui_cter.py | ||
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+ | 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, | ||
+ | |||
+ | If these files are not present, the program will simply display a warning, and you can continue. | ||
+ | |||
+ | [{{ : | ||
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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. | ||
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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 | + | ; Trial00_micrographs_ |
- | ; Trial00 micrographs | + | ; Trial00_micrographs_ |
- | ; Trial00 partres | + | ; Trial00_partres_ |
- | ; Trial00 partres | + | ; Trial00_partres_ |
- | ; Trial00 thresholds.txt : Applied thresholds for each parameter | + | ; Trial00_thresholds.txt : Applied thresholds for each parameter |
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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) |