spider.rst

SPIDER

• Website: https://spider.wadsworth.org/spider_doc/spider/docs/spider.html
• Conventions: ZYZ, standard

• Coordinate system & header description
• Doc file description
• Supported image formats: spi. Use CP for conversion. See more for TIFF import, GATAN CCD import
• 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.
• Rotation matrix:

[[cos phi,sin phi, 0],[-sin phi,cos phi,0],[0,0,1]]
[[cos theta, 0, -sin theta],[0, 1, 0],[sin theta, 0, cos theta]]
[[cos psi,sin psi, 0],[-sin psi,cos psi,0],[0,0,1]]

• Be careful when using WEB! If a volume is displayed in Web as slices, the observed rotations will be, COUNTERCLOCKWISE for 'phi' and 'psi' rotations around Z-axis and CLOCKWISE for 'theta' rotation around Y-axis. Web displays a volume with first slice on top.
• Conversion between SPIDER and Relion: link1, link2

Case of RCT

After tilt pair picking in Web you will get dcbXXX file for each tilt pair with determined angles:

dcbxxx:  (Data common to the tilt pair)

 ; dat/dat  dcb000.dat   Mon Jun 20 10:30:16 2011

 ;  Key: 121                    #Markers-fitted   #Backgrounds
 0121 6        0    0    0    0      14             0

 ;  Key: 122   Fitted-flag
 0122 6          1

 ;  Key: 123    Untilted-X,Y-Origin      Tilted-X,Y-Origin   Img-Reduction
 0123 6          382          214      406.683      245.944       1

 ; Key: 124 Tilt-angle  Untilted,tilted-axis-dir (Theta, Gamma,Phi)
 0124 6      50.3053     -78.7234     -77.8619      0    0      0

In line with key 0124 you have tilt angle θ (theta=50.3), next two angles define the angle between Y-axis and tilt axis for untilted and tilted micrograph, respectively (let's name them Psi_unt=-78.7 and Phi_tilt=-77.8). If you perform alignment of untilted stack in Spider (e.g., AP SR) you will get a file with shifts and rotations. In-plane rotation angle is in the first register. Let's name it Psi_unt_align=149.07 etc.

;; ali/hbl   17-Feb-01  AT 21:34:26 ../doc/DAL004.hbl
;    1 4  149.07     0.67946    -0.47203
;    2 4  170.17     0.13753     -2.6509
;    3 4  189.85     -5.1422     -6.7959

Now make the following calculations:

• Change sign of Psi_unt_align (see note 4)
• Subtract Psi_unt from new Psi_unt_align (to align tilt axis and Y-axis)
• Now the result of previous operation is copied to Phi_final. Check if this angle is in 0-360 range (subtract or add 360, if necessary)
• Use one of BP RP program with the following input angles (in exact order): Psi=Phi_tilt, Theta=theta, Phi=Phi_final