Polska

Strona Główna

Printable Version

Back to Previous Page

Release Notes


Release 7.7.0 is the last version of Scigress Explorer (CAChe). Scigress Explorer and Materials Explorer will be integrated into new suite: SCIGRESS.



Scigress Explorer 7.7.0

  • New in the release:

    • Adds support for the Windows Vista operating system.

    • Replaces MOPAC with MO-G.

    • Replaces MOS-F with MO-S.

Scigres Explorer 7.6.0

  • New in the release:

    • Fujitsu introduces support for Linux server platforms in Scigress Explorer 7.6. Now from a Windows platform with Scigress 7.6 installed, you can submit calculations to a centrally located Linux server. Scigress Explorer GroupServer running on either Red Hat Enterprise version 4 or SuSE version 9 is both fully tested and supported.

    • Communication between the Scigress Explorer client and the server platform is carried out using the secure shell (ssh) protocol which employs encryption of the user's password to provide enhanced network security.

    • Parallel execution of the semi-empirical molecular orbital program, MOPAC, is available for multi-processor Linux servers running OpenMP.

    • MOS-F, the new semi-empirical molecular orbital program with enhanced features for UV spectroscopic analysis, introduced in release 7.5, is now a standard component for all version of Scigress Explorer (Standard, Professional and Ultra). MOS-F, however, is the only component not currently supported with the new Linux port.

  • Fixed in the release:

    • Submitting a high volume of jobs (100 or more) to the GroupServer is no longer a problem. Previously, the communications between client and server could “lock up” and cease to return output when very high throughput was required. Current client/server tests of the GroupServer have shown that hundreds of jobs can be submitted to a Linux server without any reported problems.

    • Parameters for PM5 GroupServer calculations involving Cs and Ba are now available. Previously, GroupServer calculations involving these elements were supported only through the implementation of sparkles.

    • Intrinsic Reaction Coordinate calculations on GroupServer now run correctly, giving both the forward and reverse reaction paths.

    • ProjectLeader remains stable when multiple GroupServer jobs are submitted and the user simultaneously tries to view the chemical samples submitted to the server in the Workspace. Previously, this condition was known to cause ProjectLeader to lock up.

    • Workspace application handles errors entered into TCPCONF.txt file more robustly. Previously, the Workspace failed when information involving spurious user accounts or server platforms was entered into the TCPCONF.txt file. Now the Workspace will simply time out after a short interval if the data entered cannot be resolved.

Scigres Explorer 7.5.0

  • New in the release:

    • New module MOS-F - MOS-F version 7.0 is a semi-empirical molecular orbital program that predicts spectroscopic properties of both open and closed-shell molecules. MOS-F extends the capabilities of Scigress beyond those provided by MOPAC and ZINDO.

    • New LocalSCF 2.0 - specifically designed for fast electronic structure calculations of very large, complex proteins. This latest version includes the following new features and enhancements:

      • New support for transition metals using d orbitals within the MNDO, AM1, PM3 and PM5 semi-empirical methods.

      • All atom quantum mechanical modeling of enzymes and DNA-transition metal complexes available for hundred thousand atom systems.

      • Energy calculations and geometry optimizations possible in gas- or solvated-phase.

      • Low resource requirements provided by using localized molecular orbitals for the protein and delocalized orbitals for the transition metal portion of the system.

      • New, computationally efficient, initial guess for the wave function of DNA/RNA systems.

      • New, reliable identification of structural errors in DNA/RNA structures.

      • New analytic energy gradient for improved geometry optimizations.

      • Support for transition metals using d orbital methods.

      • Faster local geometry optimizations in solvent environment.

      • New, improved initial guess generator.

      • More reliable SCF procedure.

      • Automatic control of memory consumption - orbital tidying.

      • A powerful Cartesian coordinate to PDB converter.

      • Bond order analysis for very large systems.

    • Scigress 7.5 restores the ability to use the same version of molecular mechanics that was available in Scigress 5.0. The MM2_V5 or MM3_V5 parameter set can be selected within Mechanics Setting dialog of the ProcedureEditor. This selection can be made for any experiment that uses Scigress Mechanics.

CAChe 6.1.12

  • New in the release:

    • A new license key is required to install release 6.1.12.

    • New property, electrostatic potential on van der Waals surface, provides more intuitive coloring for electrostatics. Red indicates the most positive areas and blue indicates the most negative areas, similar to the colors on the terminals of your car battery.

    • New optional Spartan style coloring for electrostatics that can be selected at the bottom of the Tabulator Settings panel.

    • The latest MOPAC version: MOPAC 2002 v2.5.0.

    • New “LAST” keyword recovers the previous MOPAC settings used on a chemical sample. It has been added to the standard procedures for the verify transition state and find reaction paths Workspace experiments, that are found under Property of: reaction and transition states. After refining a transition state, it is important to use exactly the same method (e.g., PM5), multiplicity and solvent field settings, etc., for these two subsequent steps. However, it is all too easy to not do so, leading to erroneous results. Now, when these experiments are run, these standard procedures automatically use exactly the same settings that were used in the last calculation on the chemical sample, minimizing the possibility for error. If the last calculation was not a MOPAC calculation (Tabulator calculations are ignored and skipped over), then the standard settings are used.

    • The default setting for the solvent effective radius (RSOLV) in all MOPAC procedures using COSMO simulation in water has been changed from 1.0 to 1.3 A, as recommended in the MOPAC manual.

    • MOPAC keywords are now printed to the Workspace Experiment Status window at the start of a MOPAC calculation, allowing users to verify the settings immediately, without waiting until the end of the calculation.

    • New, improved MOPAC PM5 parameters for Ti, Cr, Fe and Cu, labeled “Fujitsu, October 2004”.

    • New MNDO, AM1 and PM3 parameters, completing all of the main group elements.

    • New, more accurate, polarizability calculations in MOPAC for H, C, N, O, F, Cl, Br and I.

    • New MOPAC procedures added to ProjectLeader to calculate polarizability (previously, only DGauss procedures were available).

    • All regression analysis tools in ProjectLeader now use the same method to calculate r(CV)2, allowing direct comparison of results from different analyses.

    • The keywords CUTOF1 and CUTOF2 have been added to all procedures involving MOZYME geometry optimizations. These cutoffs control how various one- and two-electron integrals and electrostatics are computed. They have been added with a reduced value of 7 A, which will result in faster calculations without significantly affecting the accuracy.

    • The keywords OPT_TYPE LENIENT and MICRO 1 have been added to all procedures involving DGauss geometry optimizations. To determine the optimal step length to take along the direction of the displacement vector, the DGauss geometry optimizer by default performs a line minimization in this direction. If it cannot find a point on this line at which the energy is lower, the optimizer will fail. This can especially be a problem if the potential energy is flat since the noise in the numerical algorithms employed within DGauss can obscure the search for an optimal geometry. Previous DGauss versions did not use a line minimization. These keywords disabled the line minimization and allow DGauss to reliably optimize geometries.

    • A general warning now appears when users try to open or save non-CAChe files to alert the user to check the chemical sample. For example, in certain circumstances the SYBYL MOL and MOL2 file translators may incorrectly assign atom charges.

    • The following enhancements are specific to the ActiveSite add-on to WorkSystem Pro:

      • All docking experiments return a map containing some of the lowest energy poses.

      • Co-crystallized ligands present in the PDB file are returned in the maps containing the best docked poses.

      • Enhanced PMF protein atom-typing now correctly designates sulfur as a hydrogen bond donor, even when hydrogen atoms are not added.

      • The Workspace Dock into Active Site window and the Workspace and ProjectLeader Experiments now use a consistent set of default settings for FastDock.

      • Two new ligand-protein docking properties have been added to ProjectLeader: score a ligand's currently docked geometry and optimize a ligand's currently docked geometry. These complement the existing property, dock a ligand into an active site.

      • The Workspace docking experiments have been reorganized to be consistent with those in ProjectLeader.

  • Fixed in the release:

    • Several bug fixes to the IR spectral tool.

CAChe 6.1.10

  • New in the release:

    • New analysis tools for QSAR and QSPR (e.g. best single, double, triple regressions).

    • New “SMOOTH” keyword in MOPAC removes artifacts in 3D potential energy surfaces with two search labels.

  • Fixed in the release:

    • Various bug fixes.

CAChe 6.1.8

  • New in the release:

    • Mapfile containing lowest energy poses is now created with flexible/flexible docking calculation.

    • New property, Lambda max far UV-Visible (to 150nm) added to ProjectLeader.

    • New procedures for UV-vis calculations using Molecular Mechanics and MOPAC geometry optimizations.

    • Improved explanations and help on some menu items, e.g. new Help window for the Adjacent Surface Pocket command, improved explanations in the Dock into Active Site window.

    • New checks and warnings before confirming execution of some menu commands, such as when “Beautifying” a large molecule is likely to destroy the tertiary structure.

    • “Extreme atom properties” for QSAR and QSPR, e.g. hydrogen atom with highest partial charge, carbon atom with highest susceptibility to electrophilic attack, etc.

    • Ability to change the amount of memory allocated to Gaussian jobs.

  • Fixed in the release:

    • Various bug fixes.

CAChe 6.1.1

  • New in the release:

    • FastDock option for ActiveSite offers automated docking of ligands into protein active sites using Lamarkian genetic algorithm.

    • PMF (Potential of Mean Force) method using patented enhancements for scoring docked poses.

    • ProjectLeader for automated batch docking of libraries of ligands into a series of proteins.

    • Automated batch 2D to 3D conversion when importing MDL SDF files into ProjectLeader.

  • Fixed in the release:

    • Various bug fixes.

CAChe 6.1.0

  • New in the release:

    • The new add-on, ActiveSite, supporting automated docking of ligands and compound libraries is a available as an option for WorkSystem Pro.

    • For WorkSystem Pro, CAChe includes a new version of the Getting Started tutorial that includes two new chapters on the use of ActiveSite automated docking for structure-guided drug design.

    • The new command Analyze | Group RMS computes the RMS distance difference between two selected groups and labels the structure.

    • The RMS label generated when groups are superimposed has been changed to report the RMS distance difference in A after superposition. Previously, it reported the angle in radians required to rotate one group so that it superimposed on another. After superposition, the angular RMS information is available on the RMS measurements tab in the Chemical Properties Workbook view.

    • Dynamics has been changed so that calculations are run constant temperature (NVT) instead of the previous method of constant energy (NVE). Constant temperature trajectories are much more effective at scanning a potential energy surface since they climb over hills and scan the surface at roughly the same velocity whether at a potential energy minimum or maximum. An experiment for running constant energy trajectories is available from chemical sample conformations (CAChe 5.0 experiments) | dynamics trajectory | MD simulation at constant energy (MM3).

    • It is now possible to specify the Dielectric for Dynamics calculations. The dielectric is used in the evaluation of the electrostatic terms. It is available on the Details panel of the Dynamics Settings dialog that you access with the Procedure Editor. A new experiment has been provided for running Dynamics with a water dielectric under chemical sample conformations (CAChe 5.0 experiments) | dynamics trajectory | MD simulation at constant energy (MM3).

    • New commands in the Workspace allow the display of temperature factor as the radius of atoms, the color of atoms, the color of residues or on ribbons.

    • When checked, the new Workspace setting Beautify | Auto Sprout Atom Tool causes CAChe to automatically beautify the valence as structures are drawn with the Atom tool. This feature speeds the process of drawing molecules.

    • In the Workspace, dihedral angles and atom distances can now be selected for adjustment by selecting the central bond.

    • From the File | Export command of a map window in the Workspace it is now possible to export the map as a tab delimited file for import into other programs.

    • ProjectLeader now has procedures for counting hydrogen bond donor groups and water under the group count property of a chemical sample.

    • To drag selected objects in the Workspace, it is now necessary to hold down the CTRL key while dragging the mouse. This feature prevents accidental changes to geometry.

  • Fixed in the release:

    • ProjectLeader can now read chemical samples without any bonds such as files containing atoms only.

    • Energy rescaling during Dynamics calculations makes constant energy calculations much more stable allowing longer trajectory time.

    • ProjectLeader now marks the project as requiring saving when the results of an experiment are returned.

    • The number of chemical sample files that can be loaded into ProjectLeader from an Open dialog has been increased to approximately 1,000.

    • ProjectLeader cells that fail to be converted from 2D to 3D when loading SD files are marked with a footnote.

CAChe 6.0.0

  • New in the release:

    • An additional Getting Started tutorial describes how to use CAChe to perform structure-guided drug design.

    • Protein accessible surfaces color coded by hydrophobicity and hydrophillicity are created with the new Analyze | Accessible Surface command.

    • Protein crevice maps that rapidly identify potential ligand binding sites are generated with the new Analyze | Crevice Surface command.

    • Surfaces that map the active site pocket adjacent to a bound ligand simplify design of ligands with better binding are generated with the new Analyze | Adjacent Surface - Pocket command.

    • Backbone ribbon renderings as tubes, multiple threads, flat ribbons, solid ribbons, threaded spools or threaded pods are available from the new command View | Backbone Ribbon.

    • The new command View | N-C-C Trace provides a quick cylinder trace of the protein backbone.

    • Automatic sequence alignment using the Needleman-Wunsch exact pairwise alignment algorithm with a BLOSUM50 substitution matrix is invoked from the new Edit | Align menu item in the Sequence View.

    • Automatic selection of residues in one sequence that match the selection in another sequence is available with the new Edit | Match Selection command in the Sequence View.

    • Automatic selection of residues in one sequence that are the same as that at the same position in another sequence is available with the new Edit | Select Conserved command in the Sequence View.

    • The new command View | Color by Residue makes coloring residues by property in the 3D Structure window automatic.

    • The new command Edit | Find and Replace Sequences in the Sequence View enables searching for residue sequences and replacement of the residues with a different sequence. You can copy and paste strings into this dialog, permitting you to replace a single residue with an entire protein sequence.

    • The new command Options | Amino Acid Repository in the Sequence View enables you to add nonstandard amino acids to the repository.

    • The display of residues in the Sequence View has been enhanced to display more residues at a time.

    • An interface to Gaussian 03W has been added. If you have Gaussian 03W Revision B.03 or later installed on your PC, you can run experiments using Gaussian 03W directly from CAChe.

    • New commands for hiding objects simplify and speed analysis. The new commands in the 3D Structure window are View | Hide Selected, View | Hide Unselected, and View | Show All.

    • The new command View | Suppress Hydrogens hides all hydrogens bonded to carbon. It replaces the command View | Show Hydrogens. Commands now treat suppressed hydrogens as though they were displayed and had the selection state of the atom to which they are attached.

    • Automatic labeling of all H-bonds is obtained with the new Analyze | Label H-Bonds command.

    • Automatic labeling of all atoms that are too close together and potentially bumping is obtained with the new Analyze | Label Bumps command.

    • Automatic cleanup of H-bonds with new Beautify | H-Bonds command.

    • An enhanced PDB input filter that derives bonding and charge information for HET groups from templates contained in the het_dictionaryCIF.txt file in your CAChe directory.

    • Dramatic performance enhancements for large molecules. Selections, superposition and many other commands can be 10 times quicker.

    • Introduction of the Analyze menu in the 3D Structure window eases use of BioMedCAChe by consolidating analysis items under one menu and shortening other menus. The following commands have been moved to the Analyze menu:

      • Analyze | Calculate RMS Error

      • Analyze | Superimpose

      • Analyze | Superimpose Groups

      • Analyze | Chemical Properties Spreadsheet

      • Analyze | IR Transitions

      • Analyze | UV-visible Transitions

      • Analyze | Label H-bonds

      • Analyze | Label Bumps

      • Analyze | Show Surfaces

      • Analyze | Surface Attributes

      • Analyze | Surface Legend

    • The new Edit | Select Water command automates selection of all water molecules in a chemical sample.

    • The Edit | Select Neighbors command now allows you to select either neighboring atoms or complete Residues, Waters and HETs.

    • The new View | Atom Specific Color command colors selected atoms by the user specific color you assigned using the Atom Attributes dialog.

    • Significant changes in Mechanics include:

      • New atom types in MM3 and the MM3 2000 parameter set

      • New parameters in MM2

      • Enhanced atom typing

      • Distribution of charges over resonant groups

      • Enhancements in the augmented force-field especially for hydrogen bonds.

    • The move of crystal structure commands to the Edit menu: Edit | Crystal Shape and Edit | Crystal Boundaries.

    • Edit | Move Selected has replaced the Edit | Position command as an easier to understand terminology.

    • Ctrl-click and shift-click can be used interchangeably in the 3D Structure window. This eliminates an inconsistency in selection between the Sequence View and the 3D Structure window.

    • The Group Atoms dialog now allows you to create group types: amino acid, nucleic acid, hetero, water, active site, and ligand.

    • The status bar at the bottom of the 3D Structure window now displays the chemical sample net charge, atom count and empirical formula.

    • Clicking on the background has been changed to select only objects that are visible. Use Edit | Select All to select both hidden and visible objects.

  • Fixed in the release:

    • Previously, the use of the Apply button in the Crystal Shape dialog could destroy the unit cell angles. This problem has been fixed.

    • Insertion of a residue before another in the Sequence View no longer places the O atom along the peptide bond.

    • Atom names are now always written when saving a chemical sample as a PDB file. Previously, atom names were sometimes not written and the PDB file created could not be read.

    • The augmented MM2 force-field now recognizes the bond angle for water (21-6-21) and uses a bond angle of 105 degrees and a force constant of 0.630. It is no longer necessary to add the bond angle type 21-6-21 to the MM2 force-field to get good structures for water.

    • The Copy, Superimpose Sequence and Superimpose Groups commands no longer hang when applied to large molecules.

CAChe 5.0.4

  • Fixed in the release:

    • An enhanced PDB output filter now saves all essential PDB data, including residue sequence, secondary structure, and crystallographic data.

    • New “rubber-bonding” and “snap-to-atom” features make drawing easier.

    • New Workspace ToolTips and Flyby menus ease learning CAChe.

    • Faster Workspace operations speed selection and viewing.

    • A new View | Cylinders command renders selected atoms and bonds as cylinders with small atom spheres.

    • A new View | Color by Element command colors selected atoms and bonds by element color.

    • A modified View | Lines Only command now renders bonds as small radius, 3D cylinders instead of as 2D lines so that the perception of 3D structure is enhanced.

    • A modified Edit | Select Backbone command now also selects H and O atoms attached to the backbone to facilitate a better understanding of the role hydrogen bonding plays in the structure of the backbone.

    • Modified View | Lines, View | Lines Only and similar commands no longer change the colors of atoms and bonds. Use View | Color by Element to restore element colors.

    • Numerous ProjectLeader and Workspace bug fixes improve ease-of-use and reliability.

    • New MOPAC parameters with d orbitals for Sc, Ti, V, Cr, Fe, Co, Ni, Cu, Zr, Mo, Pd, Ag and Pt in the AM1, PM3 and PM5 methods.

    • MOPAC has PM5 parameters for all main group elements except for Po, At, Fr, Ra and the inert gases.

    • MOPAC no longer treats Na and K as + sparkles since PM5 parameters are available for these elements.

    • CAChe continues to use Cs and Ba to represent + and ++ sparkles except with the PM5 method. Since MOPAC has PM5 parameters for Cs and Ba, CAChe uses Fr and Ra to represent + and ++ sparkles.

    • Faster computation of frontier orbitals from MOZYME uses compressed MOs requiring less disk space.

    • MOPAC partial charges and bond orders of different conformations can now be viewed in reaction paths and maps.

    • Numerous MOPAC bug fixes and other improvements.

CAChe 5.0.2

  • Fixed in the release:

    • MOPAC energy maps so that the graph axes are no longer swapped as they were in versions 5.01 and 5.0.

    • The PDB file reader so that:

      • When reading some PDB files containing chain IDs, HOH groups without chain IDs are no longer incorrectly included as part of residues that were in chains;

      • DOD is no longer displayed in the sequence view;

      • Adding a gap at the start of a sequence and then selecting a single residue no longer hangs the sequence view.

CAChe 5.0.1

  • Fixed in the release:

    • Capped bonds in MOPAC AM1 calculations.

    • Infrequent atom rearrangements by MOPAC during geometry optimizations.

    • The sequence view hang when the residue sequence number of the first residue in a chain is 0.

    • Incorrect defaults that were applied when opening new 3D structure windows and caused molecules to be displayed in unexpected styles such as partial charge and bond order style.

    • The missing logP procedure in ProjectLeader.

CAChe 5.0.0

  • New in the release:

    • Large molecule capability - CAChe works with tens of thousands of atoms in a chemical sample.

    • Sequence View - CAChe WorkSystem Pro includes a new Sequence View that displays protein sequence, secondary structure and properties. It is also used to build peptides, to align multiple sequences, and to develop homology models.

    • Sample Properties Window - CAChe also includes a new Sample Properties Window that displays the data in a chemical sample using worksheets in a workbook. Using this powerful tool, you can display and modify data at the same time you are viewing the same information in the 3D workspace.

    • Enhanced PDB import - The full contents of Protein Data Bank files (.pdb or .ent) are imported and saved in chemical sample files (.csf). Remarks and bibliographic information may be viewed in the Notes tab of the Sample Properties Window.

    • New Workspace commands - Edit | Find, Edit | Select Neighbors, and Edit | Invert Selection ease navigation in large molecules and simplify creation of clusterbased solvation models.

    • Mechanics and Dynamics - Hydrogen bond cutoffs at the van der Waals cutoff distance and the separation of the electrostatic interactions into internal and external regions speed up mechanics and dynamics calculations on very large molecules by a factor of 10, 20 or even 50.

    • MOPAC 2002 - The major enhancement to MOPAC 2002 is the addition of PM5 - the first new semiempirical method in MOPAC since 1986. The atom limit in MOPAC 2002 has been increased to allow calculations on molecules with 20,000 atoms. AM1/d is now parameterized for three new transition metal elements: Mo, V and Pd. Computation of bond orders and the molecular orbitals of molecules with a thousand or more atoms requires a long time. The new keyword MOZPRP has been added to MOZYME procedures so that MOPAC 2002 does not return molecular orbital information for molecules with more atoms than the specified limit. MOZPRP is set to 2,000 in MOZYME procedures.

    • Gaussian file import - CAChe opens Gaussian formatted checkpoint files (.fchk, .fch) directly. Molecular conformation, basis functions (s, p, d, f), eigenvectors, eigenvalues, calculation history, total energy, calculated gradient, polarizabilities, dipole vector, dipole moments, and Mulliken atomic partial charges are imported into a new chemical sample file. To view molecular surfaces, tabulate the surface at the current geometry using the existing wavefunction.

  • Fixed in the release:

    • It is no longer necessary to set the your decimal separator to the decimal point (.).

    • CAChe can now be run with user level privileges under Windows 2000.

    • Calculations on Windows 98/Me now run much faster because the Workspace now yields the CPU when it is idle.