Tips and tricks

Speeding up calculations

• Make your EM maps smaller

  Sometimes you may get an EM map which box is much larger than the actual map. All those extra and empty voxels will slow down calculations of cross-correlation function during calculations of fit libraries and FitRestraint.

  You can remove the extra padding voxels in an EM processing software, for example UCSF Chimera

• Downsample the EM map

  Is your map low resolution but has very small voxel size (e.g. EM map at 10 A with voxel size of 1 A)? Such unnecessarily small voxel size will slow down computations.

  Downsample your EM map then in an EM processing software, for example UCSF Chimera or EMAN2.

• Use different system representation resolutions for different restraints

  Is it necessary to use atomic representation to calculate all you pre-defined restraints? If your computational running times are relatively high then you should consider choosing more coarse grained representations for specific restraints (e.g. Excluded volume restraints).

• Always run single test runs before submitting larger modelling jobs to the cluster (or even to your local multi-core cpu).