SZMAP 1.2.0

July 2013

Update to SZMAP applications.


  • Multiprocessor Support : Calculations can be performed much faster with szmap and gameplan by using multiple processor on a single machine and on different machines with the same operating system installed. Because of this and other improvements to the software, numerical results will differ slightly from those produced by previous versions and the set of points that are determined to be clashing may vary slightly. szmap is highly parallelizable—big calculations scale very well when run on large numbers of processors.
  • szmap_grid will now split out all szmap grids into separate files in one step when the options -output_all_format and -prefix are used.
  • szmap_report now supports a -resolution option to control the quality of the property maps.
  • gameplan now indicates the stabilization magnitude in the log.
  • To streamline the szmap program, the following obscure command line options have been eliminated: -only_protein, skip_modified, -protein_charge, -protein_hydrogen, -ligand_charge, -ligand_hydrogen, -charged_mol, -no_probe_data, -require_explicit, -add_neutral, -add_vacuum, -details. There are more direct ways to perform each of the functions that they controlled. The simple help for options in each of the SZMAP applications and utilities has been streamlined.
  • The WaterColor VIDA Extension has been updated so that it no longer changes the scale of gameplan results in VIDA.
  • The Quick Start chapter is now called the Tutorial and has been reorganized to improve clarity.

Bug Fixes

  • When running from a directory with a space character somewhere in the path name, gameplan is now able to find the corresponding version of szmap.
  • The naming scheme for temporary files created by gameplan has been changed to avoid a bug that interfered with reading szmap output under certain circumstances.
  • The Coulombic interaction+van der Waals (intvdw) value produced by szmap is now the minimum of the values for each of the different orientations, the same value used to determine clashes.
  • Single grid szmap calculations (for example using -apo_grids) no longer output all grid types by default.
  • To improve consistancy, clashes in stabilization results are now marked by the text “CLASH” in the atom property szmap_stbl_clash instead of szmap_clash.
  • The options section in the szmap chapter has been modified to document additional file formats supported for some operations.
  • The minimum legal setting for the szmap options -inner_dielectric and -outer_dielectric has been increased to 1.0. Lower values can lead to problems with ZAP calculations.
  • The maximum legal setting for the szmap option -zap_spacing has been lowered to 1.0. Higher values can lead to problems with ZAP calculations.

Other changes

  • This will be the last release to support SuSe 10.
  • The szmap options -point_grid, -lig_point_grid, and apo_point_grid can no longer be used to setup the calculation without doing any actual calculations. This will be fixed in a future release.

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