SZMAP 1.1.0

August 2012

Major update to SZMAP applications, utilities and VIDA extensions.

Improvements

  • The Water Orientation VIDA extension has been completely rewritten to be more capable and easier to use. szmap now generates orientation information tagged with the neutral difference free energy rather than the neutral difference enthalpy. The Water Orientation VIDA extension will recognize this difference between newer and older szmap results.
  • An new command-line program, game_plan, identifies interesting coordinates near a ligand or in a protein binding site, runs szmap and analyzes the results, producing hypotheses of various ways the ligand might be improved based on the solvent environment.
  • szmap can now use apo grids and coordinate output from previous runs with the -use_apo_from <results.oeb.gz> command line option. Combined with the new option -split_lig, a series of ligands all bound to the same protein can be easily analyzed with szmap.
  • The default grid contour levels used in the Watercolor VIDA extension for most difference grids have been changed from -0.5/+0.5 kcal/mol to -1.5/+0.75 kcal/mol to emphasize regions with the largest energy differences. VDW grids are now contoured at -2.0 kcal/mol to emphasize good contacts.Colors are now generated taking into account whether the background is dark or light.
  • By default, szmap grid calculations will now output van der Waals values and the degree to which the probe is ordered, but not the probe burial fraction. Use -results_set max to get the probe burial. At_coords calculations now produce max results by default in order to enable analysis and categorization of points.
  • It is now a fatal error in szmap and gameplan for hydrogens to be missing from the ligand or from more than 10 percent protein heavy atoms. The option -warn_if_missing_hydrogens will cause a warning to be generated, but the calculation will proceed despite the missing atoms. Proteins may have missing atoms far from the active site due to mobile side-chains or loops without affecting the results significantly. Missing hydrogens on the ligand are more problematic. But the option to override the fatal error is provided so that special cases, where there is ambiguity about whether a hydrogen is missing or not, can be handled.
  • By default, szmap now performs ligand calculations just in the regions available in the complex, speeding up -stabilization runs. A new option -restrict_calc <level> controls this behavior.
  • The set of symmetrical probe orientations available to szmap users has been expanded to include sets with 216 and 648 orientations. Setting the number of orientations higher than a symmetrical set size but less than the next higher set, will take the symmetrical orientations and pad out the remainder with random orientations.
  • szmap now clearly identifies different output categories in the results file: complex, ligand, apo, stabilization. It also now puts the molecule plus data package previously known as ‘probe-orientation-data’ under each of these sections, renaming it ‘probe’.
  • The szmap log information printed when -verbose and -details are specified has been modified to make it easier to parse and to include more information.
  • grid_comp now supports five new operations: lig_disp and prot_disp append grids and orientation data for regions displaced in the complex by the ligand and the protein, respectively. largest returns a grid containing only the largest connected region of the source grid based on contours at a user specified level. not_mask returns data in regions that are not in the mask. offset adds a constant to each grid point. In addition, grid_comp now does a better job of describing the operations it performs.
  • pch now produces output even if -ligand_res <RES> was specified but the given residue name was not located in the input molecule. It also now supports the options -ligand_resnum <num>, -ligand_inscode <char>, -ligand_chain <char>, and -ligand_model <num> allowing you to more specifically identify which residue is to be written to the ligand file.
  • pch now supports the -fix_elements option which instructs the program to attempt to substitute elements that will work in szmap (such as Zn) for those where MMFF vdw parameters are not defined (such as Hg).
  • pch now supports the -nonsymmetrized_charges option to generate AM1BCC partial charges where topologically equivalent atoms—think methyl protons—are not required to have the same charge. The default charge-symmetrized AM1BCC charges are recommended for any workflows down the road where the ligand conformation is subject to change.
  • pch now writes out waters in the input if the -output_waters <filename> option is specified.
  • szmap_report now supports the option -tag_set <set> to provide more control over the output when no tags are specified. The tag set v1 provides backward compatibility with szmap 1.0 output.
  • szmap_report now supports the option -keep_hydrogens to force the rendering of all explicit hydrogens.
  • Version, release, platform, etc. information for szmap and related programs is now written to the display only when the -verbose flag is used or when the command is run without arguments. The status of your SZMAP license is now included along with the other information.
  • On Windows, the installer now adds the OpenEye bin directory to the environment path to better support the use of alternative command shells.

Bug Fixes

  • SZMAP vida_extensions and tutorial_files are now installed inside a version-specific sub-directory: openeye/examples/szmap/{szmap-version}/.
  • A bug that caused pch to treat reduced cysteine residues (CYS) to be charged as if they were oxidized (CYX) has been fixed. De-protonated cysteines (CYM) were not affected.
  • A bug that prevented pch from adding Amber charges to the C-term capping residue NME.
  • The Watercolor VIDA extension has been modified so that it can be run multiple times successfully on a given set of szmap output.
  • The length of the OH bond in szmap probe waters has been reduced by 0.001A so that the water probe geometry is identical to that of TIP models.
  • szmap can now save molecules with the -charged_mol flag to .oeb and .oeb.gz files.
  • A bug that prevented CLASH tags from showing up in szmap stabilization results for -at_coords calculations has been fixed.
  • The minimum number of orientations in szmap is now 2. The previous version allowed 1 orientation but the calculations would fail. Note that runs with less than the default of 60 orientations are likely to give poor energies.
  • Fixed a minor bug in the calculation of probe fractional buried surface area in szmap.
  • szmap_grid generates a more complete report describing SZMAP data in the input.
  • szmap_report provides clearer error messages when it does not find SZMAP data in the input and the -verbose flag now works properly. It also renders text at a larger, easier to read size.
  • The manual has been updated to fix a large number of typographic errors and oversights.

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