- Website: https://github.com/I2PC/xmipp-portal/wiki
- Conventions: ZYZ, standard
- Coordinate system & header description
- Note about header values
- Supported image formats
- Euler angles: (φ,θ,ψ). Positive rotations of object are clockwise. Projection direction is defined by (φ,θ). ψ is in-plane rotation for tilted image. For untilted ψ=φ=in-plane rotation. Sometimes you can find the following angles in XMIPP: rot=φ, tilt=θ, gamma(or psi)=ψ.
- Rotation matrix:
r11 = cos(psi)cos(theta)cos(phi) - sin(psi)sin(phi)
r12 = cos(psi)cos(theta)sin(phi) + sin(psi)cos(phi)
r13 = -cos(psi)*sin(theta)
r21 = -sin(psi)cos(theta)cos(phi) - cos(psi)sin(phi)
r22 = -sin(psi)cos(theta)sin(phi) + cos(psi)cos(phi)
r23 = sin(psi)*sin(theta)
r31 = sin(theta)cos(phi)
r32 = sin(theta)sin(phi)
r33 = cos(theta)
where the first index refers to rows and the second to columnsAfter tilt pair picking in Mark utility you will get untiltX.ang file for each tilt pair with determined angles (in folder Preprocessing/untiltX):
# alpha_u alpha_t gamma
75.783 74.6211 55.9613In this line you have tilt angle gamma=55.9, the previous two angles define the angle between Y-axis and tilt axis for untilted and tilted micrograph, respectively (alpha_u=75.78 and alpha_t=74.6). Cut particle images will be rotated at later step so that the tilt axis is parallel to Y axis. If you perform 2D-alignment of untilted stack in XMIPP (e.g., ML2D) you will get a doc file with shifts, rotations and other parameters. In-plane rotation angle is in the third register. Let's name it Psi_unt_align=358.25 etc.
; Headerinfo columns: rot (1), tilt (2), psi (3), Xoff (4), Yoff (5), Ref (6), Flip (7), Pmax/sumP (8), LL (9), bgmean (10), scale (11), w_robust (12)
; /home/conical/Images/untilt1/untilt1_000001.xmp
1 12 0.00000 0.00000 358.25000 0.00000 1.00000 39.00000 0.00000 1.00000 -22479.67578 0.00000 0.00000 0.00000Now if you use RCT in xmipp_protocols the program will do the following:
- Assign rotations, X and Y-shifts for untilted stack (psi_unt_align from ML2D, Xoff, Yoff)
- Center tilted stack with align_tilt_pairs command.
- Copy alpha_t to Psi_final, copy Psi_unt_align to Phi_final, copy gamma to theta.
- Make a 3D reconstruction using the angles (Phi_final,**theta**,**Psi_final**) from previous step for tilted images.