SpectraProcessing

fft of the projection has been calculated we must run the spectra program in order to determine the position of the reflections in the Fourier domain.

Specifically, two important actions are carried out with Spectra:

1. The indexation of the lattice, that is, the generation of the indices that fix the lattice points.
2. The determination of the lattice vectors in the fourier domain.

This information is included in the output file

Indexation of the lattice and determination of the lattice vectors

• In the Spectra tool Bar we go to file-open-file.fftand then select suitable magnitudes for X+ ( 250), Y+ ( 250) and Y- ( 150).
• Then , In the Spectra tool Bar we go to Tools-display controlsand select suitable magnitudes for X+ ( 250), Y+ ( 250), Y- ( 150), low ( 0), high ( 100), Magnitude ( 2), spot radius ( 2) and scale ( 2). The resulting image is displayed below

/spectra1.jpeg

• Now, we determine the lattice vectors in the fourier domain. However, before we do this, we will calculate the theorical dimensions of this vectors by using the following Xmipp commandxmipp_lattice_vectors -lattice_a [0,64] -lattice_b [55.42,-32] -crystal_size 1024 -ang 120.00 -60.00 70.0 which yields

 a  =(0,64) (64) b  =(55.42,-32) (63.9951) ap =(-20.5918,-36.9862) (42.332) bp =(-39.5434,15.0972) (42.3274)  Angle from ap* to bp*=98.2103

• The vectors of our interest are the ones highlighted in blue. To select the coordinates of these vectors in the lattice we go to Tools-image query. This action displays a window where the coordinates of the mouse in the lattice are shown. A small red circle is drawn in the lattice when a point is selected. The resulting image is shown below

/spectra2.jpeg

• According to the blue vectores shown above, we must choose the right indices for the red circles of the figure. Specifically, the top circle should have the coordinates (-4, 0), whereas the bottom red circle should have the coordinates (0, -6)

• Once we have indexed the lattice we go to Tools-lattice refinement-refine and see the profile of the lattice as shown below

/spectra3.jpeg

Evaluation of the lattice refinement and generation of ouput files

• We can study the accuracy of the lattice refinement that we have just carried out by checking data information - lattice parameters. The coordinates of these vectores should match (with a reasonably high precission) the vectors calculated with Xmipp _lattice_vectors (shown above in blue).

• Finally, we generate the ouptut files that contain the information of the indexes of the lattice and the lattice vectors. To do this, we go to Tools - MMBOX refinement. Please note the value of the script parameters Istep ( 25), Imaxcor ( 25) and Threshold ( 0.13).

-- Main.JavierRodriguez - 12 Mar 2007