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September 1997
(c) Copyright 1997 MDL Information Systems, Inc. All rights reserved.
Welcome to the 2.1.3 release of ISIS/Base and ISIS/Draw.
The main focus of this release is to support Japanese operating
systems on Windows 95 and Windows NT 4.0. New PL intrinsics have
been added, and also many selected defect corrections have been
made to ISIS/Base and ISIS/Draw.
This file gives important information about the 2.1.3 version of
ISIS/Base and ISIS/Draw. Please refer to the other readmes included
in this package for information about areas such as installation, the
ISIS/Application Development Kit, the Add-In Manager and Add-Ins, and
the specialized database applications. Readmes are included to list
customer-reported defects that have been corrected in this release.
To access all 2.1.x functionality, you must be running ISIS/HOST 2.1.x
or later. For ISIS/Draw and ISIS/Base 2.1.x, you can use the 1.3.x or
later version of ISIS/Host. If you are using ISIS/Host 1.3.x, the
following ISIS/Base features will not be available to you and should
not be used:
* Calculated fields
* Hierarchical sorting over remote databases (sorting on
non-root-level fields)
* List manipulations
* New extreg prompting features
* Reaction query highlighting
* New SD/RD File features (merge, merge overwrite)
* Some performance-related features (packet size setting)
With non-postscript printers, the quality of your printed documents may vary
with the quality of your printer driver.
The installer will install the version of the program that is
appropriate for your platform. ISIS/Base is delivered as two files on
the 32-bit Windows version -- ISISLib.dll and Ibase32.exe -- and as
two files on PowerPCs -- ISISBase_PPC (application) and ISISBaseLib
(in Extensions folder) to support the Object Library.
A single installer installs the basic desktop software and the
The installer on the Macintosh will delete the following preference
files from the preferences folder:
ISIS/DRAW Add-in Manager
ISIS/BASE Add-in Manager
These preference files store the customization of the Add-Ins
installed via the Add-In Manager and will be lost after the
installation to correct an incompatibility.
We do not support running 16-bit Windows ISIS on Windows95 or
WindowsNT nor do we support running 68k ISIS on PowerPC Macintoshes.
ISIS 2.1.3 installer prevents the user from installing on NT3.5.1.
Our software is only compatible with versions 4.0 or later on WinNT.
Notes for ISIS/Draw Users
In addition to a few selected defect corrections,
the following changes are included in ISIS/Draw 2.1.3:
ISIS/Draw hotlink to ChimePro has been added for the Macintosh
Chemscape Chime is a Netscape Navigator plug-in that allows
users to view chemical information directly in a Netscape Navigator
HTML page. ISIS/Draw supports a hot-link where right clicking on a
chemical structure box displayed in a HTML page using Netscape
(rendered in 2D) will display a pop-up menu. Selecting the
Edit/Transfer to ISIS/Draw menu item will automatically launch
ISIS/Draw (if it is not already running) and transfer the sketch into
a new ISIS/Draw sketch window. When the link is established, a
hot-link tool appears on the left side of the horizontal toolbar
displaying the link icon. ISIS/Draw can then be used to edit the
sketch. Pressing the hot-link tool in ISIS/Draw updates Netscape with
the sketch from ISIS/Draw and makes Netscape the active application.
Please note that in order to paste a sketch from ISIS/Draw into a
Chime structure box, you need to check the "Copy Mol/Rxnfile to the
Clipboard" setting located in the General tab of ISIS/Draw's Settings
dialog. In ISIS 2.1.2 this functionality is now also enabled for the
for the Macintosh platforms.
The following notes describe new functionality introduced in ISIS/Draw
2.1.1/2.1.2. These notes are added for the convenience of the users who
have not upgraded to ISIS 2.1.1 or 2.1.2 yet.
We added a new hot-link tool on the toolbar for displaying the linked
server's icon . When an ISIS/Draw sketch object is linked
or embedded into a client application, such as Microsoft Excel,
double clicking on the sketch object launches ISIS/Draw (if it is not
already running) and transfers the sketch into a new ISIS/Draw sketch
window. When the link is established, a hot-link tool appears on the
left side of the horizontal toolbar displaying the icon of the client
application. ISIS/Draw can then be used to edit the sketch. Pressing
the hot-link tool in ISIS/Draw updates the client with the sketch from
ISIS/Draw and makes the client the active application.
With ISIS/Draw, you will be able to display an informative text
string in the ToolTip for each of the ten customized template tool
buttons. You can customize the ToolTip text by saving the template
file with a text string in the Name field located in the Save
Name/Comments dialog. This dialog can be accessed from the Save As
dialog by clicking on the Save Name/Comments button. The text saved
with the template file will appear in the ToolTip when the cursor is
passed over the custom template tool. Note that if the Name field in
the template file is changed during a Draw session, Draw must be
restarted in order to reinitialize the new string into the
Rgroup Attachments can now be easily created via the keyboard and the
atom tool. To create a Rgroup attachment, select an atom and type:
*1 to add a primary attachment point (->*)
*2 to add a secondary attachment point (->*")
*12 or
*1,2 to add double attachment points (->* and ->*")
*0 to delete attachment point(s)
We no longer support the Publish & Subscribe functionality on the
Macintosh for ISIS 2.1.1 or higher. The following Publish & Subscribe
menu items will no longer appear under the Edit menu in ISIS/Draw:
Create Publisher...
Publisher Options...
Subscribe To...
Subscriber Options...
Show Borders
Although the menu items will not appear in Draw 2.1.1 or higher, the
underlying code still remains in Draw. The menus can be added back using
PL for those customers who wish to use Publish & Subscribe.
Known Issues In This Release of ISIS/Draw
The following discrepancies are known in ISIS/Draw:
ChemCheck may report overlapping atoms even though the atoms don't
appear to overlap. To correct the situation, increase the distance
between the offending atom(s) and it's neighboring atom(s), then rerun
ChemCheck. If the overlapping atoms warning appears often, you may
want to turn off the overlapping atoms warning message in the
ChemCheck tab located in the Settings dialog. (CW-21368)
ISIS/Draw does not support sprouting from inside polymers, mixtures or
formulations brackets. Currently, ISIS/Draw does not prevent the user
from doing so and may lead to crashes. Sprouting from atoms outside
the brackets is fully supported.
Repeated IAC of queries containing multiple groups will create duplicate
of the repeat in the multiple group (cw23381). This will be fixed in
ISIS 2.1.4.

Notes for ISIS/Base Users

On the Macintosh, if there is not enough memory to load a shared
library, there is a system error message suggesting the library could
not be found. On the PowerPC Macintosh, ISIS/Base currently has two
parts, one of which is a shared library. If there is not enough
memory to load this library, you will see the message: "The
application ISIS/Base 2.1.3 could not be opened because ISISBaseLib
could not be found."
Known Base-ISIS For Excel Issues in This Release
If you need to run ISIS For Excel and ISIS/Base at the same time, start
ISIS For Excel first.
Known Host-Base Issues in This Release
TCP/IP packet size for ISIS/Base 2.0 access to ISIS/Host 2.0 is
limited with TGV Multinet v. 3.3 and 3.4. TCP/IP communication
between ISIS/Base and ISIS/Host occurs in discrete packets of a
predetermined size. With the release of ISIS/Base 2.0 and
ISIS/Host 2.0, the packet size can be set by the user in sizes
between 512 and 4096 bytes. During prerelease testing, it has
been found that packets larger than 512 bytes were not transmitted
correctly when an OpenVMS VAX was using TGV Multinet versions
3.3 and 3.4 for TCP/IP communications. The underlying problem was
traced to TGV Multinet libraries not behaving correctly. Until TGV
corrects the underlying problems in their TCP/IP ISIS/Base users will
be required to use a different library or set the TCP/IP packet size to
512 (which is the default). (CW-17215)
A number of ISIS/Base features require ISIS/Host 2.0.1 (rather than
ISIS/Host 2.0) for correct operation.
There have been customer requests to change the "*atom searching".
Any single atom query will return all structures containing * atoms.
This search feature will be changed a forthcoming release of ISIS/Host
in 1997.
Several issues have been corrected in ISIS/Host 2.1.1 (VMS) and
2.1.2 (Unix). These include:
SB-01095 Host "flips" brackets sometimes with Orient
SB-01242 Data Sgroup mapped to wrong field during SSS
SB-01264 Error during highlighting of Sgroup structure causes
MCATCH error. This issue is addressed in the next
release of ISIS/Host.
SB-01260 Update of an existing structure containing a * atom
Causes a crash.
Compatibility Issues For ISIS/Base
Problems with large fonts have been observed with several Windows 3.1
display adapters. Should you encounter cut-off text, try changing to
the small font. (CW-19561)
We have encountered unstable behavior with some resolutions on some
display adapters. Should you encounter frequent crashes with a
particular display adapter, try changing to a different resolution.
CCMail's CCNotify Control Panel interferes with ISIS/Base searching on
the Macintosh. (CW-20326)
Lotus Notes 3.2 is reported to interfere with Page Layout in
ISIS/Base. This problem is corrected with Notes 4.0. (CW-22550)
Known Issues In This Release of ISIS/Base
The following issues are known in ISIS/Base:
If you save a list in a local database in ISIS/Base PC or Mac,
it cannot be opened in versions prior to 2.0.2. This is caused by
changes to enable storing larger lists than previously. (CW-21510)
You cannot run more than one instance of 16-bit Windows ISIS/Base at
one time in Windows. A utility, IBLaunch, has been developed to
enable running more than one instance. The utility, along with a
document that describes its use, is installed with the 16-bit Windows
version of ISIS in the same directory as ISIS/Base.
To ensure referential integrity, database administrators should ensure
that linking fields are marked as not updatable in Oracle databases.
SDFiles should only be used for moving data from one molecule
database to another molecule database. In all other cases, RDFiles
should be used. In particular, when the database has any hierarchical
elements, only RDFiles will faithfully transmit the data.
On the Macintosh, behavior in low memory situations can be unstable.
Low memory is more common when large molecules (>1200 atoms and bonds)
are manipulated. Try increasing the memory partition allocated to
Large structures (> 1200 atoms and bonds) cannot be transferred from
Base to Draw on the Macintosh due to system limitations. If the sketch
is too large to be set via the link, it will return an error message
indicating the problem. (CW-17639)
In Windows 3.1 systems, the maximum number of cells in a form is now
2700. It was 3500 in prior releases. This limit does not apply on
Macintoshes and does not apply in the 32-bit Windows version.
The 32-bit Windows version supports larger sketches or structures than
the 16-bit version does. (CW-21131)
Exporting CFS SDFiles when the form has multiple modelstructure boxes.
The Export CFS SDFile capability was originally implemented for forms
with a single modelstructure box containing the query. When more than
one model- or modelstructure box is present in the form, users should
adjust the form so that the CFS query box (highlighted during the
search) has the highest sequence ID of any model/modelstructure box in
the form. This will ensure correct operation of Orient/Highlight
features and correct translation of fitted models onto query
coordinates. This can be achieved by: In Forms mode, double click
the query box, pick Function tab, and for Sequence ID enter the
highest value, then click OK and resave the form. (CW-20342)
To export a form file from a Macintosh to the PC, press and hold down
the Option key while you highlight Export on the File menu, and choose
Form from the cascading menu. To import a form file from a PC to the
Macintosh, press and hold down the Option key while you highlight
Import on the File menu, and choose Form from the cascading menu.
Then release the Option key. Next, always use the Text Translation
setting in the Apple File Exchange program to transfer Macintosh form
files to the PC format or vice versa. Activate the Replace CR with
CR/LF check box, and set the Special Characters and Tab Characters
(This also applies to exchanging SDfiles, RDfiles, molfiles, and
rxnfiles between the Macintosh and the PC.) (CW-03963)