
Accelrys ViewerPro Trial Edition Version 5.0  (6/12/2002)
Release Notes - Microsoft Windows NT / 98 / 2000 /XP

(C) Copyright 2002 Accelrys Inc.  All rights reserved.

 Thank you for your interest in the Accelrys DS ViewerPro. We think 
 you will like this powerful 3D molecular visualization and chemical 
 communications tool and look forward to hearing your comments and 
 suggestions. 

			--- The ViewerPro Team


=======================================================================
        Preview Edition
=======================================================================

 This version of the Accelrys DS ViewerPro is an evaluation copy. It is
 completely functional for 30 days from the time you install it. After 
 that time, the ViewerPro will no longer run. If you like the software, 
 please consider purchasing it from Accelrys Inc. by visiting us at 
 http://www.accelrys.com/viewer/. 


=======================================================================
        Supported Computers
=======================================================================

 This document covers the Accelrys ViewerPro running on Windows 98, 
 Windows NT, and Windows 2000, and Windows XP computers. For Windows 
 NT systems, you *MUST* have version 4.0 with Service Pack 3 or greater 
 installed.  For Windows 98, you *MUST* have Windows 98 Second Edition. 
 For Windows 2000, Service Pack 2 is recommended.


=======================================================================
        What's New
=======================================================================

 in Version 5.0

  - Atom, Protein, and DNA/RNA Display Style toolbars
  - Protein secondary structure assignment is done with the Insight II
    secondary structure analyzer
  - Invert atom works for pyramidal nitrogen atoms
  - Labels can use any installed True Type font
  - Monitors can use different fonts
  - Isosurfaces now have Quad Mesh and Volume Display Styles, and a 
    Display Style page
  - Hydrogen atoms added to crystal waters, or any un-attached atom are 
    added in randomized directions
  - Surface by context
  - Text Annotations now use Label Display Style page
  - Ribbons and Surfaces are now affected by the Options Quality choice,
    and can be rendered in much higher resolution
  - Tube backbone display for DNA/RNA
  - Color atoms by Isotropic Displacement (Temperature Factor)
  - Centroid Monitor

  - In DS ViewerPro 5.0, add-on modules are also available:
    - DS ViewerPro Enterprise enables the ViewerPro to access data 
      in the ProjectKM database
    - DS Property Calculator calculates Lipinski rules, and many others
    - DS Molecular Overlay provides targeted and consensus rigid and 
         flexible molecular alignment
    - DS Conformer Generation calculates new conformation using 'kicks'
         in torsion or coordinate space

 in Version 4.2

  - CIF file reader now supports mmCIF
  - Support for PNG file export
  - PDB file reading speed increased by 2/3
  - MSV file reading speed increased by 50%
  - Disulfide bridges are now shown in appropriate protein displays
  - VRML output improved
  - Quanta file importer improved
  - SMILES import and export now supports cis/trans stereochemistry
  - MSI file importer now reads version 4 files with proteins correctly

 in Version 4.0

  - Multiple light sources
  - Clipping Planes
  - Function keys to switch mouse modes
  - Text Annotation, Text Box Annotation, Text Callout Annotation tools
  - Add Polar Hydrogens and Show Hydrogens commands
  - New Stereo Window command
  - Split screen stereo command
  - Enhanced Edit/Properties dialog box (edit-in-cell)
  - Enhanced DataTable (edit-in-cell, multilevel sorting)
  - BumpMonitor now uses intrinsic hydrogens in determining bumps
  - HBondMonitor now detects hydrogen bonds to external atoms when set 
    on a selected set
  - Surfaces now has Display As WireMesh, rather than Display As Dots
  - ProteinSequence objects in the Datamodel
  - Protein display on aminoacid ranges
  - Restore Default options
  - Fit-to-View is now sensitive to selection
  - Molecule-centered rotations 
  - Option page to set default display style on import
  - Paste From Location command

 in Version 3.7

  - "CAlpha" color scheme for proteins
  - Scaled Ball and Stick atom display style
  - Cylinder and Sphere performance enhanced by 2
  - Tile Molecules in Window command
  - SMILES file import
  - Program loading speed improved
  - Ultra-high quality option for graphics
  - Enhanced syntax in SetProperty command (element != Carbon)
  - Enhanced Hydrogen Bond Acceptor query feature
  - Objects in Hierarchy Window show selected children
  - Hierarchy Window maintains expansion state

 in Version 3.5

  - Supports hardware stereo
  - Enhanced protein secondary structure analysis, and display
  - Enter Command dialog
  - Molecular Alignment
  - Structure Monitor
  - Intelligent Hierarchy Window tiling
  - Enhanced Screen Annotations
  - SelectByRadius command for scripting
  - Measure button
  - File/Open shows all molecule types


=======================================================================
        General Installation Instructions
=======================================================================

 CD-ROM Installation:

 1. Close other Windows applications.

 2. Insert the Accelrys DS ViewerPro CD in your CD-ROM drive.

 3. Choose the "Install the DS ViewerPro" button on the setup program 
    that automatically runs. If the setup program doesn't automatically 
    run, or if you have CD autorun turned off, double-click on the 
    Setup.exe program in the root directory of the CD, or double-click 
    on the Setup.exe program in the Install directory.
 
 4. Follow the directions given during the setup procedure.

 5. The installation takes less than two minutes to complete. The Start 
    menu contains an entry entitled "Accelrys DS ViewerPro 5.0", and a 
    DS ViewerPro shortcut is placed on your Desktop.  If you prefer not 
    having the shortcut on your Desktop, you can delete it--the Viewer
    is not deleted by deleting the shortcut. 


 Internet Installation (download):

 1. Close other Windows applications.

 2. Double-click on the exe file that was downloaded. 
 
 3. Follow the directions given during the Setup procedure.

 4. The installation takes less than two minutes to complete. The Start 
    menu contains an entry entitled "Accelrys DS ViewerPro 5.0", and a 
    ViewerPro shortcut is placed on your Desktop.  If you prefer not 
    having the shortcut on your Desktop, you can delete it--the Viewer
    is not deleted by deleting the shortcut. 


=======================================================================
        Installed system files
=======================================================================


 The following libraries are installed for all versions of Windows:

	File		   Version			Description
	atl.dll		3.00.8449		ATL Module for Windows (ANSI)
	mfc42.dll	6.00.8665.0		Microsoft MFC Shared Library
	msvcirt.dll	6.00.8168.0		Microsoft C++ Runtime Library
	msvcrt.dll	6.10.8581.0		Microsoft C Runtime Library
	msvcp60.dll	6.00.8168.0		Microsoft C++ Runtime Library

 In Windows 95 only, which does not come with OpenGL by default, the 
 following are installed:

	OpenGL32.dll	4.00		OpenGL Client DLL
	Glu32.dll	4.00		OpenGL Utility Library DLL

 All of the libraries are the most current available from Microsoft. The
 installer checks the version of the libraries when it attempts to do the 
 installation, and does not install any library over a newer version.


=======================================================================
        Other goodies on the CD
=======================================================================

 o  From the autorunning Setup.exe program in the root directory of the
    CD, you can also install the Accelrys Screen Saver. Choose the 
    "Install the Screen Saver" button on the setup program. The Screen 
    Saver installer is in the \Gifts\Screen Saver directory on the CD.

 o  You can read the Getting Started Manual by choosing the "Getting
    Started Manual" button in the setup program. The Getting Started
    Manual is an HTML document on the CD, in the \Help\GettingStarted
    directory. Double-click on the "Index.html" file to read. 

 o  We have provided a large number of sample molecule files of many
    different file formats in the \Molecules directory. These are
    grouped according to type.
 

=======================================================================
        Running the Accelrys ViewerPro
=======================================================================

 The Accelrys DS ViewerPro can be started via the Start menu.  A 
 shortcut is placed on your Desktop that can be used to run the 
 ViewerPro. 

 Setup installs some interesting molecules in the ViewerPro's default 
 directory.  

 Please consult the DSViewerPro.chm file for more information regarding 
 operating the Accelrys DS ViewerPro. You can also access help from the 
 Help Topics command in the Help menu while in the DS ViewerPro. 


=======================================================================
		Known Problems and Limitations
=======================================================================

 1. On Windows NT, depending on how your system is set up, Administrator
    privileges may be necessary to install the DS ViewerPro.

 2. Users of the ViewerPro on Windows 2000 should be set up as "Power
    Users" to prevent an error writing program preferences to the 
    Registry: "Failed to update the system registry. Please try using 
    REGEDIT." 

 3. If you received a beta or preview version of the Accelrys 
    DS ViewerPro 5.0, make sure you un-install it before you install 
    this version of the Viewer.

 4. QUANTA files containing fractional coordinates cannot be properly
    read into the Viewer.

 5. When specifying a file from the command line, provide the file's
    path and name (e.g., MSViewer .\arg.pdb).

 6. A molecule pasted into an OLE container (such as Word) is printed 
    in low resolution. The workaround to this problem is as follows:  
    resize the frame around the pasted molecule so that it is as large 
    as possible. Then, in-place activate the molecule by double-clicking 
    on the molecule, rotate the molecule just slightly, then de-activate
    it by clicking outside the in-place frame in the OLE container 
    application. This causes the Viewer to send the OLE application a 
    bitmap with greatly increased resolution (it takes longer to copy 
    the bitmap, and the resulting file is larger because of the larger 
    bitmap). At this point, resize the embedded molecule to the proper 
    size and it will retain the higher resolution bitmap. Note that, if 
    you re-activate a pasted molecule at the smaller size, the smaller 
    bitmap is re-copied to the container.

 7. If you sketch a molecule that has a resonance delocalized hydrogen
    directly as an aromatic ring (such as imidazole), the Viewer does 
    not add a hydrogen to the nitrogen atoms properly. A consequence of
    this is that the Gasteiger charging algorithm cannot calculate the
    correct charge for the nitrogen atom. If you sketch imidazole as 
    a Kekule structure with two double bonds, the Viewer properly 
    adds hydrogens, and if Perceive Aromaticity is turned On when 
    Clean Structure is executed, hydrogens are also added correctly 
    to the aromatized structure, and the partial charges are calculated
    correctly. Once the structure is aromatized, if you want to create 
    the other tautomer, create the alternate Kekule structure and 
    allow Clean to aromatize it.

 8. All standard Catalyst function definitions are imported, exported,
    and visualized correctly. OR queries are imported, but not exported
    or visualized properly.

 9. A script can run other scripts. However, you cannot create a 
    looping script, for instance, script #1 runs script #2, which 
    then runs script #1. This eventually causes the Viewer to run 
    out of memory.

10. The SMILES importer in the Viewer has occasional problems 
    interpreting the chiral specification when the chiral center is 
    at a ring closure bond.

11. By default, usage of graphics hardware acceleration is turned off
    so that most graphics cards work properly.  If you have a graphics 
    board that accomodates hardware acceleration, better graphical
    performance and appearance can be obtained by un-checking the
    "Disable graphics hardware acceleration" check box in the General
    page of the View/Options command.

12. The DS ViewerPro now uses compressed HTML (CHM) format for the
    online help document. If you had a previous version of the ViewerPro
    where you associated CHM files (Catalyst files) to the ViewerPro,
    you may have problems viewing the help document. To fix this problem, 
    un-install the earlier ViewerPro. You may re-install it, only don't
    associate the CHM file to the ViewerPro -- this only affects
    loading those files into the ViewerPro via a double click, it does
    not affect reading them directly using the File/Open menu.


=======================================================================
        Questions or Problems
=======================================================================

 If you have questions or problems with the Accelrys ViewerPro, first 
 consult the online help file.

 If you find a software bug and wish to report it to Accelrys, please 
 write to us at support@accelrys.com. We will make every attempt to give
 you a reply quickly with a workaround or other information about your 
 problem.

