CTF-based Tuning Parameters Dialog

This dialog allows you to set parameters that are used when taking images for routines that do CTF fitting, namely, when calibrating and correcting astigmatism, correcting coma, and taking a Zemlin tableau.  By default, Record parameters are used for these images.  The upper part of the dialog lets you change the Record parameters in specific ways.  The bottom of the dialog has options governing how the routines initially determine and modify focus.

Set exposure to X sec

Select this option and enter an exposure time to use in place of the one in Record parameters.

Set drift settling to X sec

Select this option and enter a drift settling time to use for the images.

Set binning to N

Select this option and enter a binning to use for the images.  The CTF analysis itself should be fairly insensitive to binning unless it is too high, but you may want to use a binning higher than 1 to make the Thon rings extend farther out in the display. The program will find the nearest available binning.  For K2/K3 cameras, the program will use a binning of at least 1 if this option is not selected.

Use full-field images, not current subarea

Select this option to use the full camera area regardless of any subarea set in Record perameters; this will generally give the most signal for CTF fitting.

Align frames with N frames

Select this option to use frame alignment with the Framealign module in SerialEM or the SEMCCD plugin to DigitalMicrograph if the camera supports taking frames, and enter the number of frames to acquire.  If this option is off, frame alignment will not be done, regardless of the setting in Record parameters.

Align with parameter set N

Select this option to use a specific frame alignment parameter set instead of whatever is specified in Record parameters, and enter the position of the set in the table in the  Frame Alignment Parameters dialog (numbered from 1).

Find initial defocus with Focus area in Low Dose mode

For the astigmatism and coma operations, the program needs to know what the defocus is so that it can set the fitting range correcting for the CTF routines. If necessary, it will measure defocus using beam-tilted images as usual.  By default, it does this on-axis with Record images when in Low Dose mode, to give the most accuracy by measuring at the same location where CTF will be measured.  Select this option to use the Focus area instead, if you are trying to minimize dose at the current location.

Smallest defocus allowed for correcting astigmatism

The program will make the defocus more negative, if necessary, to have a minimum amount of underfocus when measuring or correcting astigmatism.  Enter a minimum value here; the default is -0.9 micron and a value as small as -0.1 micron is allowed.

Amount to increase underfocus when calibrating astigmatism or measuring coma

Astigmatism calibration and coma measurement require a larger defocus to allow for the astigmatism in the beam-tilted images.  This entry specifes the increase in underfocus; the default is 0.5 micron and a value as small as 0.2 is allowed.