gEMpicker Notes

  • Supported input formats: CCP4 for micrographs and templates, TIFF for masks
    • Micrographs: all *.map files in the directory dirTgt
    • Templates: all *.map files in the directory dirSch
    • Masks: all *.tif files in the directory dirMsk
  • Output results are stored in the directory dirRes
    • dirRes/pik_coord: position of picked particles from each micrograph
    • dirRes/pik_ext: all particles picked from each micrograph
    • dirRes/xcorr: correlation maps
  • Using CUDA:
    • Supported compute capability: sm_2x, sm_3x
    • Supported CUDA Toolkits: 4.0, 5.0
    • Required packages for NVIDIA GPU driver from Ubuntu's Package Manager
      • CUDA 4.0: nvidia-settings and nvidia-current
      • CUDA 5.0: nvidia-settings-updates and nvidia-current-updates
    • CUDA Toolkit installation
      • CUDA 4.0: nvidia-cuda-toolkit from Ubuntu's Package Manager
      • CUDA 5.0: the programs assume that the CUDA Toolkit 5.0 has already been installed at /usr/local/cuda/, if the toolkit has been installed in another place, a symbolic link to the toolkit's installation by using sudo ln -s your_install_dir /usr/local/cuda/ is needed
    Please contact Thai Van Hoang if you want to run gEMpicker on a cluster using MPI.