Average FragMaps

The average between SILCS FragMaps of structurally similar proteins can be used to identify ligands that bind bind to those proteins. The SilcsBio software provides a utility in the command line interface (CLI) to calculate the average over two or more sets of SILCS FragMaps. Average FragMaps may be used for a qualitative understanding of regions of the proteins that will interact similarly with certain functional groups. Average FragMaps may also be used quantitatively, with caution, for re-scoring of SILCS-MC docked ligands. The two-step procedure for calculating average FragMaps is described below.

  1. Copy all the silcs_fragmaps_<protein PDB> directories you wish to use to a new directory in which the average calculations will be performed.

    Please make sure that the FragMaps meet one of the following criteria:

    • All sets of FragMaps have the same grid setup, which means the header of the silcs_fragmaps_<protein PDB>/maps/*.map files are the same.

    • All sets of FragMaps have were created relative to proteins having the same rotational and translational alignments. If the input proteins were not aligned to each other prior to running SILCS, you must use the “ref=” option with the 2b_gen_maps command to ensure alignment. A map cutting algorithm will be used to make the FragMaps compatible, with the smaller dimensions of the two grids used to calculate the difference maps.


    It is imperative that the two SILCS FragMaps used to calculate average FragMaps are oriented to structurally aligned proteins. Average FragMaps that result from incompatible FragMaps will not provide any useful insights.

  2. Generate the average FragMaps using the following command:

$SILCSBIODIR/utils/calc_average_maps.sh <path-to-directory-with-all-silcs_fragmaps_*> <silcs_fragmaps_ref>

The command will require two inputs:

  • Path and name of the directory containing all SILCS FragMaps to be averaged (<path-to-directory-with-all-silcs_fragmaps_*>). This directory corresponds to the “new directory” created in the first step.

  • Path and name of the SILCS FragMaps directory containing the reference PDB structure (<silcs_fragmaps_ref>).

The average FragMaps will be saved in a directory AVG_MAPS and can be visualized in the same way as standard FragMaps (Visualizing SILCS FragMaps). When visualizing the average FragMaps, the FragMaps will be overlaid onto the reference PDB structure specified in the second step.


The FragMaps MUST be for highly homologous proteins and MUST be generated by using the most common structure as reference for the structural alignments.