====CTFAPPLY====
** By Vinzenz Unger and Anchi Cheng**


his program corrects the phase data of an individual image for the “contrast transfer function” and astigmatism where applicable. It should be pointed out that CTFAPPLY assumes a square image, which is different from programs involved in the cross-correlation and unbending procedures. Hence, no CTF correction can be applied if the original image is rectangular.

As illustrated in Fig.6 the contrast transfer function modulates the image transform in a sinusoidal manner.

images/fig6.png
Using the unit cell parameters, the absolute value of the CTF can be calculated for each diffraction spot if the image size, pixel size, magnification, accelerating voltage, spherical aberration of the objective lens and the amount of underfocus are known.. As described earlier the amount of underfocus can be estimated from the position of the Thon rings if these are visible in the transform. If the image is astigmatic, then the Thon rings will adopt an elliptical shape in most cases. The amount and direction of astigmatism can be described by providing the underfocus along the two major axes of the ellipse and by specifying the angle between one of these axes and the x-axis of the transform. The convention used by CTFAPPLY is that the specified angle refers to the amount of underfocus that is listed first, i.e. “df1 df2 deg”. The angle is positive if the line that connects the transform origin with the pixel that was used to calculate “df1” points to the right and counterclockwise from the x-axis of the transform. The amount of underfocus specified by “df2” will be applied in a direction perpendicular to “df1”. The values for “df1” and “df2” will be identical if the image is not astigmatic. In this case the setting for the angle is arbitrary. However, in all other cases the range for setting the angle “deg” is ±90˚. The program will calculate the appropriate value if the specified angle lies outside the expected range. Application of the CTF will result in contrast reversals - i.e. addition of 180˚ to the raw phase - for all reflections whose calculated CTF values are negative. In addition, the calculated values of the CTF will be written out for all reflections (last column in the output file) to allow a correction of image-derived amplitudes at later stages if necessary. It should be emphasized that the CTF values are an indispensable tool in the refinement of the defocus values for each image. Therefore, the use of TTBOX (see below) to obtain CTF-corrected phase values should be limited to the data from images of highly tilted crystals, where no reasonable raw data can be obtained by MMBOXA due to the observed splitting of reflections.

As for MMBOXA a film identifier number is an input requirement for CTFAPPLY. The current version expects the last digit of this number to occupy the 10th column from the left hand margin. Missing digits will be automatically filled in by zeros whereas overflowing digits will be automatically truncated. The exact positioning of the number is important in this case because ORIGTILTD, which is “downstream” of CTFAPPLY checks the number against a second copy of this number (see comments for ORIGTILTD) in the ORIGTILTD command file to assure that the intended and actual image are the same. While “odd” at first sight, this feature is useful, especially when handling larger data sets where film serial numbers can be very similar in many cases.