Task 3 : gEMfitter – Very Fast Cryo-EM Density Fitting


About

gEMfitter is a template-based highly parallel GPU-accelerated program for multiresolution fitting of macromolecular structures developed at INRIA Nancy. It runs in multi-thread and multi-process mode to use all avaliable CPU cores and GPUs in a single workstation or a multi-node cluster for the demanding 3D correlation computation.

Download
http://gem.loria.fr/gEMfitter.html
 
Supported input formats
  • CCP4 for search and target maps

Example result
Fitting individual chains into a GroEL-GroES map at 23.5 A resolution
 
Method
  • Uses same parallel CPU+GPU framework as gEMfitter
  • Uses GPU texture memory to accelerate rotations
  • Normalized corelation functions (NCCs) give best performance with low resolution maps
  • Similar quality to "COLORES'", but ~ 1000x faster (GPU/CPU)
 
Reference

Thai V. Hoang, Xavier Cavin, and David W. Ritchie, gEMfitter: A highly parallel FFT-based 3D density fitting tool with GPU texture memory acceleration. Journal of Structural Biology, 2013.  Full Text.