CTF Assessment: GUI tool to assess and sort micrographs according to their CTF parameters estimated by sp_cter.
Usage in command line
Standard usage: sp_gui_cter can be run as a stand-alone program or run from the SPHIRE GUI:
Upon startup, the following windows will appear:
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.
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.
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:
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.
To apply these thresholds, click on Apply All Thresholds in the Control Panel. A pop-up dialog box will appear, asking you confirm whether to apply the thresholds. The deselected files will no longer be checked in the micrograph list, and the Selection Summary at the top of the Control Panel will be updated with the current number of total and deselected micrographs.
Clicking on Save Selection will write out the following files:
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 format of
partres.txt is changed. The old format is also supported for now, but will be removed in near future. Please also refer sp_cter.
Category 1:: APPLICATIONS
Beta:: Under evaluation and testing. Please let us know if there are any bugs.
There are no known bugs so far.