ChemBio3D Ultra 11.0 with MOPAC
 The
ChemBio3D Ultra 11.0 suite includes ChemDraw Pro 11.0, ChemBio3D Ultra 11.0
, Chem3D interfaces to Schrödinger’s Jaguar and Gaussian, GAMESS
Pro 11.0 , MOPAC 2002 Pro, ChemFinder Std 11.0, ChemDraw/Excel, E-Notebook
Pro 11.0 and the ChemDraw and Chem3D ActiveX Pro Controls & Plugins.
ChemBio3D Ultra 11.0 brings workstation-quality molecular graphics and rigorous
computational methods to your desktop, allowing you to explore the structure
of large chemical and biological models. The Structure Browser is a new
tool for viewing sets of small structures and their properties for analysis
and comparison. *(W = Windows Only)
Applications Included
- ChemBio3D Ultra 11.0
This ultimate application for desktop molecular modeling and state-of-the-art
protein visualization is designed for both Chemists and Biologists.
Visualize detailed 3D protein-ligand complexes and DNA structures using
open GL graphics and stereo hardware and display and analyze Hydrogen
bonds and partial surfaces. Build small molecules using the ChemDraw
interface and see the 3D structure appear simultaneously, perform basic
Molecular modeling computations such as Alignment, Dihedral driver
MM2 experiments, Molecular Mechanics with support for MMFF94.and Dynamics.
Perform ab initio and semi-empirical calculations, and predict and
visualize NMR, IR and Raman spectra with interfaces to MOPAC, Jaguar
GAMESS and Gaussian.
- MOPAC Pro 11.0
MOPAC is a general-purpose semi-empirical quantum mechanics package
for the study of chemical properties and reactions in gas, solution,
or solid-state. This premier molecular computation application features
a number of widely-used, semi-empirical methods and allows you to compute
properties and perform energy minimizations, optimize to transition
states, and compute properties. It supports MOPAC sparkles, has an
improved user interface, and provides faster calculations.
- GAMESS Pro 11.0
Chem3D Ultra provides a graphical interface to the GAMESS program for
ab initio quantum chemistry. A variety of wavefunctions (RHF, ROHF,
UHF, GVB, and MCSCF, CI and MP2 energy corrections) and basis sets
are available. Users can also calculate vibrational frequencies and
a variety of molecular properties, such as dipole moments, hyperpolarizabilities.
GAMESS is maintained by the members of the Gordon research group at
Iowa State University
- ChemDraw Pro 11.0
In addition to basic chemical structure drawing, this premier application
provides Chemical query properties, , the ability to create and edit
templates and nicknames, Annotation, Relative Stereochemistry, ISIS/Draw
Compatibility, support for ISIS-style Data SGroups, Chemical File Formats,
Expansion of Generic Structures, TLC Plate Tool, the new Freehand Pen
Tool, Fragmentation Tools, PolymerDraw, ChemProp, Structure Cleanup,
calculation of Topological Polar Surface Area as well as the ability
to read and write a wide variety of chemical file formats including
spectra and reactions.
- ChemDraw/Excel Pro 11.0
ChemDraw/Excel allows the user to create chemically knowledgeable spreadsheets
within the familiar Microsoft Excel environment. You can build and
manipulate chemical structures within Excel, compute chemical properties
and perform database searches.
- ChemFinder Std 11.0
ChemFinder Std is a database management system appropriate for anyone
who works with chemical information and chemical structure databases.
Browse, create, search, and update databases with structural, numeric,
and text data via user-customizable forms, including structural and
sub-structural queries, as well as linking to related data in sub-forms.
View and edit structures in a variety of modes, automatically create
databases and forms for imported data, export and print.
- E-Notebook Pro 11.0
E-Notebook Pro allows users to maintain configurable lab journals with
pages from ChemDraw, Microsoft Word, Excel, PowerPoint and spectral
software. Search by structure and text, Draw reactions in ChemDraw.
E-Notebook performs stoichiometric calculations dependant upon the
reaction and other entered parameters. Retain a complete Audit trail
of experiments at each save, including username and timestamp, share
prewritten protocols that automatically add data from experiments using
AutoText.
- ChemDraw ActiveX/Plugin Pro 11.0
This premier ActiveX Control/Plugin allows you to query online databases
and view & publish online structures. This installer will automatically
install the necessary Plugin or ActiveX controls based on your web
browser(s). It adds save and print abilities to ChemDraw ActiveX/Plugin
Net.
- Chem3D ActiveX Pro 11.0
This premier ActiveX Control/Plugin allows you to view & publish
online structures in 3D. This installer will automatically install
the necessary Plugin or ActiveX controls based on your web browser(s).
It adds save and print abilities to Chem3D ActiveX/Plugin Net.
Applications Features
(W) - Feature available on Win only
Chem3D
- 3D Glasses
(W) Included glasses provide enhanced stereo-mode with depth shadings
to give realistic 3-dimensional quality to all Chem3D renderings. (Included
in CD-ROM purchases only.)
- Automatic Overlay
(W) Select multiple molecules and let Chem3D automatically align them
with a target molecule.
- ChemDraw LiveLink
(W) Simultaneous 2D & 3D editing! Draw structures using a ChemDraw
window embedded in the Chem3D application. This powerful feature adds
a 2D view that is always in-sync with the 3D view.
- ChemProp
(W) Advanced property parameter including BP, MP and more.
- CLogP
(W) CLogP property server provides the latest methodology for calculationg
n-octanol/water partition coefficients.
- Dihedral Driver
(W) New conformational analysis tool allows the generation of MM2 energy
plots.
- Enhanced Graphics
(W) Chem3D uses openGL to provide high quality graphics display.
- Formal
Charges
(W) Assign Formal Charges to Atoms and Chem3D will generate delocalized
charges automatically.
- GAMESS Interface
(W) Chem3D interface to GAMESS.
(Note: GAMESS application is required. See applications included section
to clarify.)
- Gaussian Interface
(W) Chem3D interface to Gaussian.
(Note: Gaussian application is required. See applications included section
to clarify.)
- Group Labels
(W) Display group labels in the Chem3D model view.
- Hydrogen Bonds
(W) Automatically display hydrogen bonds in the 3D view!
- Kekule / Delocalized
Display Mode
(W) Toggle between dashed line and alternating single-double bond representation
of delocalized and aromatic bonds.
- MM2
(W) Built in support for MM2 to generate realistic 3D structures.
- MMFF94
(W) MMFF94 is a molecular mechanics force-field that supports both organic
molecules and biopolymers. MMFF94 force field provides a richer set of
atom types than MM2.
- Model Explorer
(W) Hierarchical tree-control for exploring the structure of large models.
Import a PDB file and examine chains, groups, and ligands. This new feature
gives fine-grained control.
- Molecular Modeling & Dynamics
(W) Workstation quality molecular modeling.
- MOPAC Interface
(W) Chem3D interface to MOPAC. (Note: MOPAC application is required.
See applications included section to clarify.)
- Partial Surfaces
(W) Generate and display partial surfaces for protein active sites.
- PowerPoint
(W) Embed Chem3D models in PowerPoint files. Rotate and zoom Chem3D models
while giving a presentation.
- Schrödinger Jaguar Interface
(W) Chem3D interface to Schrödinger Jaguar, an ab-initio calculation
package. (Note: Jaguar application is required. See applications included
section to clarify.)
- Spectrum Viewer
(W) Display spectral calculation results from Jaguar, Gaussian, and GAMESS
as a graphical display in a separate window.
- Stereo Hardware Support
(W) Use Chem3D with a variety of stereo monitors, shutterglasses, & other
hardware to provide a true 3-dimentional modeling experience.
- Structure
Browser
(W) Allows users to easily scroll through a collection of small molecules
and compare their structures and properties.
ChemDraw
- ActiveX Edit in ChemDraw
Edit your document using your installed version of ChemDraw, rather than
your ActiveX, providing greater screen real estate for editing, and also
access to the full range of ChemDraw capabilities.
- Annotations
Store annotations to include additional reference data for each structure
or object in your drawing. Annotation data ranges from manually entered
text to attached documents, literature references or links.
- Atom Numbering
Add sequential numbering indicators to atoms in a structure.
- Chemical
File Format
Reading & writing of chemical file formats including spectra & reactions.
- Chemical
Warnings
Mouse-over red box to read error description.
- Color Faded Shapes
Shapes can now be filled with a faded color.
- Custom Templates & Nicknames
Ability to create & edit templates & nicknames.
- Expand Generic
Structure
Generate multiple structures from an "abbreviated" generic
structure.
- Floating Character Map
Add special characters from any font instantly to any ChemDraw document.
- Floating
Periodic Table
Element information available at all times with floating periodic table
on the desktop.
- Freehand Drawing Tool
Use the mouse or other pointing device to draw freehand shapes using
this intuitive drawing tool.
- Graphic Display & Image
Adds greater detail to on-screen drawings and saved image files.
- Graphical
File Formats
Import graphics stored in GIF, TIFF, PNG, JPEG, and BMP formats.
- I/Draw
Mode
New compatibility mode allows ChemDraw to look and feel like your legacy
drawing package.
- Improved Molecule Clean-up
A completely revised molecule clean up tool rearranges structures in
a more consistent way across a wider spectrum of structure types.
- ISIS-style
Data SGroups
Data can be attached to objects.
- LabArt
Publication-quality EPS glassware art for use within your ChemDraw documents.
- Mass & Other
Fragmentation Tools
Three fragmentation tools: Mass, Dissociation, & Retrosynthesis.
- MDL
Molfile
Read and write files in the Molfile format.
- MS Office Integration
(W) ChemDraw offers full integration via OLE, so you can embed your drawings
in any Office document.
- Multi-Page Docs
Create multiple page documents and posters within a single ChemDraw file.
- New
Arrows Tool
Control every aspect of arrows drawn, including arc, length, headstyle,
dipole, no-go and more.
- Object Specific Settings
Create drawings with different styles in different parts of the document.
- Online
Menu
(W) Draw a structure or model and immediately get online vendor information
ChemACX.Com with the click of a button.
- Polymer Draw
Represent and manipulate polymers in ChemDraw.
- Properties LiveLink
Chemical names, formulas, molecular weights, and other physical properties
added to the document are “live”, and will now update automatically
as modifications are made to structural diagrams.
- Relative Stereochemistry
Allows specification of relationships between groups of stereocenters
smaller than an entire molecule.
- SD File Format Support
Import and export SD files directly from ChemDraw.
- Stereochemistry
Identifies stereocenters using Cahn-Ingold Prelog rules.
- Structure CleanUp
Improves poor drawings.
- Structure Drawing
Draw chemical structures.
- Structure Perspective Tool
Adjust the perspective of ChemDraw molecules with simple horizontal/vertical
mouse movements.
- Terminal Carbon Labeling
Automatic display of atom labels on terminal carbon atoms.
- TLC Plate Tool
Customizable and crescent-shaped spots available from TLC tool for reproduction
of TLC plates for inclusion in ChemDraw Documents.
- tPSA
Topological Polar Surface Area (tPSA) provides a fast approximation of
the molecular polar surface area, a useful parameter for prediction of
drug transport properties, which has been show to correlate with human
intestinal absorption and blood-brain barrier penetration.
ChemFinder
- ActiveX Control Boxes
(W) Include third party ActiveX controls on your ChemFinder form.
- Automatic
Form Generation
(W) Automatically build or extend databases by importing structures from
collections of structure files, databases, SDFiles, or other sources.
- CAL
Programming
(W) CAL is a simple programming language, accessible to non-programmers
allows automation, self-running demos, custom operations; includes debugging
features.
- ChemFinder/Office
(W) Search on your computer or network for chemical
structures in Word, Excel, Powerpoint, ChemDraw, ISIS files and more,
and browse, search, refine, or export your hit list to any destination.
- Chemical
Searching
(W) Search for (sub)structure, similarity, numeric values, text, chemical
formula (including element ranges, element exclusions), date. Support
for tautomers and alt groups.
- Hit List and Query Management
(W) Use a navigation tree to track history of searches between sessions,
allow queries to be rerun or reconstituted; merge lists by drag-and-drop
in tree. Queries color-coded to relate to BioViz plots.
- List Merge
(W) Merge hitlists with any logic: intersect, union, subtract, reverse
subtract.
- Multiple Data Views
(W) View records one at a time, in a table view or a multiform view.
- Subforms
(W) Link relational data to your main table via subforms.
- Tabbed Forms
(W) Partition a form into sections using tabbed form pages.
E-Notebook
- Audit Trails
(W) Retain a complete copy of the experiment for each save, including
username and timestamp.
- AutoText
(W) Share prewritten protocols that dynamically add data from the experiment.
- ChemDraw & Stoichiometry
Calculations
(W) Stoichiometric calculations are long and tedious. E-Notebook tackles
this troublesome problem by performing the calculations for you, dependant
upon the drawn reaction and other entered parameters.
- Configurability
(W) Design forms and add buttons that are tailored to your needs. (multiple-user
configuration only)
- Document Pages
Pages contain Excel spreadsheets, Word documents, ChemDraw drawings,
spectral data, images and PowerPoint slides.
- Extensive Data Types
(W) Notebook pages include ChemDraw reaction schemes, Microsoft Word
and Excel documents, and spectral data using the Galactic
- Spectral Control.
Microsoft Office & Galactic Spectra
(W) E-Notebook manages all the other kinds of data chemists store in
their notebooks. For free-form data, you can include Microsoft Word or
Excel documents. For spectral data, you can take advantage of the Galactic
Spectral Control embedded in the noteboo
- Multiple Projects
E-Notebook combines all your notebooks into one. Organize project notebooks
the way you work.
- Retrieval
Search by structure, keyword, dates and other types of data.
System Requirements
- Windows 2000, XP, Vista (32-bit only); Excel add-ins require
MS Excel 2000, 2003, or XP
- Mac OS X 10.3.x PowerPC, 10.4.x PowerPC, 10.4.x
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