Generationofcrystals

Generation of a crystal

To generate a crystal we must define its corresponding lattice vectors. Once the lattice vectors are chosen, the lattice, i.e. the crystal, is completely determined.

In the following file, , we show the crystal dimensions, 2048 Amstrongs, the lattice vectores, each of them has 128 Amstrongs and formed an angle of 120º, and different options and noises that can be applied to the crystal

Crystal Parameters --------------------------------------------

Crystal dimensions

2048 2048
Lattice vector a

0  128
Lattice vector b

110.85 -64
Shift noise

0.1
Disappearing threshold (1=All features appear)

.98
Orthogonal projections

No
File with shifts, put null if not available

NULL

Generating the projections of a crystal

To obtain the projections of a crystal (which features are described in the file afforementioned) we must use the following xmipp command xmipp_project -i

The content of the file (where the spatial position of the projections are determined)

# Volume and projection files ------------------------------------------------
# volume description file or volume file

# projection seed and extension (this last is optional)
proj 1 spi
# Y and X projection dimensions
128 128
#
# Angle Set Source -----------------------------------------------------------
#Externally generated
 rot tilt psi 
#
#Internally generated
#0 0 1
#-60 60 13
#0 0 1
NULL
# Noise description ----------------------------------------------------------
#     noise (and bias) applied to rotational angle 
0
#     noise (and bias) applied to tilting angle 
0
#     noise (and bias) applied to psi angle 
0
#     Noise (and bias) applied to pixels 
8
#     Noise (and bias) applied to particle center coordenates 
0

Visualization of the projections

The output of the command xmipp_project -iis a set of projections of a crystal which format is "spider". These projections can be visualizated by using the xmipp command xmipp_show -img

-- Main.JavierRodriguez - 12 Mar 2007