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This folder contains simulated EM Single Particle data and its corresponding generation parameters. 

All the simulated 'particles' are generated by the software package 'InSilicoTEM'*.

This folder is sub-divided into 2 parts: 
The 'mrcs' folder contains 10000 particles 'picked' with relatively low center precision**. 
The 'params' folder contains document file which keeps record of all simulation parameters. Which are:
defocus: defucs value, in (um)
xshift : the image shift on x-axis (if you open it in imod, plus sign means moving upward)
yshift : the image shift on y-axis (if you open it in imod, plus sign means moving right)
alpha  : see below
beta   : see below
gamma  : the 'roll-pitch-yaw' angles in terms of Euler Angles, in (degree). Precise definition can be seen in 'InSilicoTEM'.

The projected protein is GroEL, PDB code '4HEL'.(http://www.rcsb.org/pdb/explore/explore.do?structureId=4hel).

Several EM simulation conditions which might be in use:
Acceleration Voltage:      300 kV
Thickness of the specimen: 38 nm
Spherical aberration:      2.7 mm
Chromatic aberration:      2.7 mm
Illumination aperture:     0.00003 rad
Energy spread:             0.25 eV
Dose:                      50 e/A^2
DQE & MTF:                 the same with FalconI camera
Angstrom per Pixel:        1.42 A
Diameter of objective aperture: 100um

The EMX file containing information of particle parameter is generated by the script "convertParamToEMX_ver2.1.py".

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*  : Reference: M.Vulovic et al., Journal of Structural Biology, Volume 183, 2013. This software simulates TEM image formation of (macro)molecules by 'taking into account the interaction potential, microscope aberrations and detector characteristics'.
** : Ranging from -20 ~ +20 pixels in terms of center shift. 
     To simulate the experimental defocus situation, every 200 particles are grouped into one. Every group shares the same defocus value, equally distributed from -2.3um ~ -3.3um.
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Technical Support: Yuchen Deng (Doctoral Candidate, Prof. Fei Sun's Lab)
Mail-to:           feisun@ibp.ac.cn        (Prof. Fei Sun);
                   frederyk1989@gmail.com  (Yuchen Deng);
Tel:               +86-010-64888137

Institute of Biophysics, Chinese Academy of Sciences
Address: 15 Datun Road, Chaoyang District, Beijing, 100101, China