Hybrid LocScale
^{Reference-based local sharpening with a partial model}

The hybrid LocScale workflow is useful in cases where partial model information is available but substantial map regions of interest or contextual densities cannot be modelled and/or are likely to fall outside the model generalisation of EMmerNet, or in cases where optimal local sharpening using a physics-based amplitude scaling procedure is desired.

Hybrid LocScale workflow

Usage

locscale -hm path/to/halfmap1.mrc path/to/halfmap2.mrc -mc path/to/model.pdb -v -o model_based_locscale.mrc --complete_model

Here, halfmap1.mrc and halfmap2.mrc should be the unsharpened and unfiltered half maps from yourr 3D refinement. If you wish to use the full map instead, use the following command:

locscale -em path/to/fullmap.mrc -mc path/to/model.pdb -v -o model_based_locscale.mrc --complete_model

Note that in this case no half map validation can be performed for coordinate and ADP refinement of the hybrid model.

Recommended use of unfiltered input maps

Note that using unfiltered maps as input is essential. Information beyond the spatial filter cutoff cannot be recovered.

Point group symmetry

If your map has point group symmetry, you need to specify the symmetry to force the pseudomodel generator for produce a symmetrised reference map for scaling. You can do this by specifying the required point group symmetry using the -sym/--symmetry flag, e.g. for D2:

locscale -hm path/to/halfmap1.mrc path/to/halfmap2.mrc -mc path/to/model.pdb -v -sym D2 -o model_based_locscale.mrc --complete_model 

The output will be a locally sharpened map scaled according to the refined atomic B-factor distribution of the hybrid atomic/pseudoatom model.

Speed-up computation on multiple CPUs

To speed up computation, you can use multiple CPUs if available. LocScale uses OpenMPI/[mpi4py (https://mpi4py.readthedocs.io/en/stable/) for parallelisation, which should have been automatically set up during installation. You can run it as follows:

mpirun -np 4 locscale -hm path/to/halfmap1.mrc path/to/halfmap2.mrc -mc path/to/model.pdb -v -o model_based_locscale.mrc  --   complete_model -mpi