Tomogram reconstruction
The reconstruction is done in Fourier space with the same algorithm as used for single particle analysis. The amount of memory required is determined by the frequency space reconstruction volume. Roughly, 20 times the size of the tomogram is needed. Exceeding this will impede all operations and the computer may have to be restarted. At the start of the program, an estimated memory requirement is calculated and checked if there is enough memory on the computer. If not, the program will abort.
btomrec -verb 1,tim -size 2048,2048,256 -scale 0.5 -resol 6 -CTF flip -rescale 0,1 -trans full -edge 2 -rec RS1_G6_01_rec.mrc -out RS1_G6_01_rec.star RS1_G6_01_ps.star
Options
- -size: Size of the tomogram.
- -scale: For non-unity scale relative to the original micrographs
- -resolution: Maximum resolution in the tomogram (in Å)
- -CTF: Contrast transfer function correction applied to a micrograph
- -rescale: Chenge the average and standard deviation to the given values
- -transform: Transform the frequency space volume to real space
- -edge: Smooth the edges of the micrographs before integration (in pixels)
- -reconstruction: Ouput reconstruction file name
- -output: Output parameter file
Most tilt series are taken at a pixel size that is much more ambitious than the final detail in the tomogram. The tomogram can therefore be calculated at a smaller scale, with the advantage of being faster and taking less storage space
The CTF correction is done for tilted images prior to incorporating each micrograph into the 3D volume