November 27, 2007 - Schrödinger is pleased to announce the second update release to Schrödinger's 2007 Suite. The update release contains enhancements and fixes for existing products and workflows.
Click here for a PDF of the Product Feature list for the second update release of Schrödinger Suite 2007. To download the update release, please visit the Download Center .
Updates to Existing Products
CombiGlide/Core Hopping 1.5.112 [Visit Product page]
• Fixed bug in Core Hopping in which 'R#' atom type in SD files that allows users to define specific attachment points on the core was not being honored when run from Maestro
Jaguar 7.0.213 [Visit Product page]
• New density functionals from Don Truhlar: M06, M06-HF, M06 L, and M06-2X
• Bug fix for the M05-2X functional (calculations using this particular functional with earlier versions of Jaguar should be re-run)
• Speedups for all density functionals containing the kinetic energy density or the Laplacian of the density, including the M05 and M06 classes of functionals, PWB6K, PW6B95, B95, and the B98 functional
• Inclusion of correction factors for the hydrogen_bond.py script when run with the ‘-fast' option
KNIME Extensions 1.0.036 [Visit Product page]
Numerous enhancements and bug fixes have been implemented since version 1.0.030. Below are some of the more important improvements:
• New nodes:
o Multiple file reader
o Nodes necessary to run Induced Fit Docking (IFD) workflow
o NMR shielding constants
o Filter Glide PoseViewer file by user-defined receptor contacts/interactions
o Generate unique (canonical) SMILES
o Download PDB structure from local repository
o GlideScore sorter
• MacroModel Ligand Torsion Search node now reports number of conformations generated
• Additional options added to the Jaguar Single Point Energy node
• Fixed bug that prevented Molecular Reader node from reading large files
• Fixed bug in Similarity Matrix node
• Fixed bug in LigPrep node that was preventing Epik from being used
• Fixed bug in RRHO Entropy node
• Fixed bug in Mae-to-SMILES node
• Fixed bug in Phase Hypothesis Reader node
MacroModel 9.5.213 [Visit Product page]
• Fixed bug in which chiralities of bridging atoms in fused ring systems were not always retained when generating ring conformations using ConfGen-based searching (e.g., Ligand Torsion Search in MacroModel and command-line driven conformational search in Phase)
Maestro 8.0.314 [Visit Product page]
• Better depth cueing through improvements to the clipping planes
• Fixed bug that prevented copy and paste of text between Maestro and other programs; now copy via selection and paste via middle mouse click now function as expected
• Better compatibility with various NFS implementations by addressing bugs related to project cleanup
• Now possible on Windows to download and update Script Center Python scripts directly from within Maestro
• Made it easier to uninstall old versions of Maestro
Phase 2.5.213 [Visit Product page]
• New shape-based screening and alignment tool to rapidly search a set of files or a Phase database against a shape query. It may be run through the command line as $SCHRODINGER/phase_shape, or using a Python GUI that is available from the Script Center.
• New tool, $SCHRODINGER/utilities/phase_hypoSimCalc, for computing a matrix of similarities for a set of Phase hypotheses
• phasedb_manage jobs are now restartable if they die as a result of hardware failure
• phasedb_manage now supports specification of an alternate title property when adding structures from a Maestro or SD file
• Indices are now created for Phase database keys at the time of site creation, which speeds up the phase_dbsearch pre-screen and record deletion operations. Indices may be created for existing databases using $SCHRODINGER/utilities/phasedb_index.
• phasedb_confsites memory usage has been reduced during the SQLite update by limiting the number of records held in memory
• Fixed bug in command-line driven conformational ConfGen search in which chiralities of bridging atoms in fused ring systems were not always retained when generating ring conformations
PrimeX 1.0.312 [Visit Product page]
• Added support for use of 'x' and 'o' as designators of test and working reflection sets
• Fixed method for determination of map extent for real-space operations
• Fixed atom typing error for N-terminal seleno-methionine
QSite 4.5.213 [Visit Product page]
• The first three items listed under Jaguar also apply to QSite
Updates to Existing Solutions/Workflows
Protein Preparation [Visit Solution page]
• Fixed several minor bugs
Virtual Screening Workflow (VSW)
• Fixed several minor bugs