ProtGctf

Jose Miguel de la Rosa Trevin edited this page May 21, 2016 · 2 revisions

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gctf - CTF estimation on GPU

This protocol is based on gctf [1], a GPU accelerated program for Real-Time CTF determination, refinement, evaluation and correction. At this moment movie options, CTF refinement for particles and tilt refinement options are not supported yet.

Input parameters

To estimate the CTF you will need to select first the Input micrographs, that can be any SetOfMicrographs produced earlier (Fig. 1). Then you can choose the frequency region to be analyzed. The limiting frequencies must be such that all zeros of the PSD are contained within those frequencies. There is a wizard, shown in Fig. 2, that helps in choosing those frequencies. To see the all available options, choose the Advanced expert level, switch to Advanced tab and click on the Help button for any specific parameter (Fig. 3).

01.ProtGctf
Figure 1. GUI input form of the gctf protocol


02.CTFWizard
Figure 2. CTF wizard helps to select a downsampling factor and the range of spatial frequencies


03.ProtGctfAdvanced
Figure 3. Advanced protocol parameters

Analyzing CTF results

The CTFs of good micrographs typically have multiple concentric rings, shown in Fig. 4 left, extending from the image center towards its edges. Bad micrographs may lack rings or have very few rings that hardly extend from the image center. A reason to discard micrographs may be the presence of strongly asymmetric rings (astigmatism, Fig. 4 center) or rings that fade in a particular direction (drift, Fig. 4 right).

04.CTFexamples
Figure 4. CTFs of good, astigmatic and drift micrographs respectively.


When the protocol is finished you may click on the Analyze Results button to show the list of micrographs and their PSD (Fig. 5). To discard micrographs with bad CTFs you may click with the mouse right button and press Disable. Once you finish the selection, press on the Micrographs button to create a subset of micrographs with only the enabled ones.

05.ProtGctfResults
Figure 5. Displaying CTF results


Sometimes the CTF estimation algorithm may fail to find the rings even if they can be seen by eye. If this is the case, you may help the algorithm to find the rings by clicking on the image with the mouse right-button and choosing Recalculate CTF on the menu that appears. A graphical interface will help you to correctly identify the CTF. You must provide the first CTF zero and the search range, and then press OK. When you finish, press the Recalculate CTFs button.

It is possible to analyze the CTF profiles by right-click on a micrograph row and selecting the Show CTF profile option which should open a window shown in fig. 6. It is also possible to analyze the CTF fitting by selecting the Display CTF Analysis option. A plot should appear with the 1D profiles calculated by gctf (fig. 7). This is an interactive plot that can be zoomed to specific regions among other things.

06.ProtGctfCTFProfile
Figure 6. CTF profile


07.CTFFitting
Figure 7. CTF fitting


References

  • [[[1]]] Zhang K. (2016). Gctf: Real-time CTF determination and correction. JSB, 193: 1-12.

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