The Arrow buttons allow each transformation parameter to be changed by a selected increment. There is an additive increment for translation, an independent increment for rotation angle, and a multiplicative factor for magnification and stretching.
The Stretch Angle slider sets the axis along which the section will be stretched by either an Arrow button or a hotkey. This axis is shown by the red dashed line. If the section has already been stretched, the axis of that actual stretch is shown with a blue dashed line.
If the program was started with "-a" to specify a Global rotation angle, this angle is displayed and can be adjusted with the spin box below the Stretch Angle slider. Use the up and down arrows to adjust the angle by 1 degree, or type in a new value directly. Select Mouse shifts X only to constrain translation changes with the mouse to the X direction in the rotated images. With this constraint, it is still possible to change the shift in Y with the arrow hot keys or the Y translation arrow buttons.
If the program was started with "-t" and a file of tilt angles, then two more controls appear. Select Apply cosine stretch to stretch the current image along the X axis by the ratio of the cosines of the current and reference image tilt angles. They should be easier to line up with this stretching. Below this checkbox is Tilt angle offset spin box to allow you to adjust the tilt angles by a constant amount. For very high tilt angles, this offset may be needed to get the right amount of cosine stretching.
Rotation, magnification, and stretch will occur around the center of rotation, which is marked by the yellow star. You can use [Ctrl]+Middle-Mouse-Button to move this center to a point that you want to keep fixed during further changes of the transformation. You can also set up a second fixed point using [Ctrl]+Right-Mouse-Button, after which stretching with the mouse will keep both the center and this fixed point at constant positions.
Correcting image stretch can be nonintuitive when done just with a regular stretch. Here is a procedure to follow using stretching with a second fixed point:
In the top panel, the X and Y radio buttons can be used to select which type of edge, if there is more than one type of edge in a section. The edge number is displayed in a spin box and can be changed by typing a new number into the text box or by pressing the up and down arrow buttons.
Only X and Y translations of one piece relative to another can be changed when fixing montages.
The bottom panel displays information about the errors in fitting pieces together with the current displacements and allows one to go to the edges with the highest error. An error is the difference (or distance) between the displacement between pieces implied by the X and Y translation values at that edge, and the displacement achieved when all pieces are shifted into best alignment using the translation values for all of the edges.
For the edges with the four highest errors, the edge number and error are displayed in a button, which can be pressed to make that edge be the current edge. The errors, and even the edges, displayed in these buttons will change whenever the displacement at the current edge is changed.
Below the buttons are the X and Y components of the error at the current edge. On the line below that is the "Leave-out" error for the current edge, which is its error when its translation values are left out when solving for the best fit between pieces. This error can be compared directly with any mismatch observed between the pieces. Pressing the Apply Leave-out Error button will change the X and Y translations by these amounts.