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7/27/2019 CS ChemOffice Ultra
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CS ChemOffice Ultra(R) version 6.0
For Microsoft Windows 95, Windows 98, and Windows NT
1999-2000, CambridgeSoft Corporation
December 13, 1999
More up-to-date information can be found at:
http://www.camsoft.com/support/
Contents of this Read Me document:
I. Before Installing
II. Software Installed with ChemOffice Ultra 6.0
III. ChemDraw 6.0 - New Features and Release Notes
IV. Chem3D 5.0 - New Features and Release Notes
V. ChemFinder 6.0 - New Features and Release Notes
VI. Uninstalling CambridgeSoft Software
VII. Software Development Kit
VIII. Technical Support
-------------------------
I. BEFORE INSTALLING
We recommend that you uninstall or delete any previous versions
of CambridgeSoft software before installing this version.
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See Section VI. for more information about uninstalling
CambridgeSoft Software.
If you have any personal stationery or templates you wish to
add to the new version, please be sure to copy your CD_Items
directory to a temporary location prior to uninstalling.
After installation, copy only your stationery (*.cts) and
templates (*.ctp) into the new CD_Items directory. Be
cautious, replacing certain files (isotopes.txt,
Nicknames.dat, etc) may cause the software to become
unusable.
-------------------------
II. SOFTWARE INSTALLED WITH CHEMOFFICE ULTRA 6.0
1. ChemDraw Ultra 6.0
2. Chem3D Ultra 6.0
3. ChemFinder Ultra 6.0
4. ChemDraw Plugin (if supported browser found)
5. Chem3D Plugin (if supported browser found)
-------------------------
III. INFORMATION ABOUT CHEMDRAW 6.0
For that latest support information for ChemDraw,
please see:
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B. Launching and Quitting
ASIAN WINDOWS NT 4.0- Launching ChemDraw under Japanese, Chinese
or Korean Windows NT 4.0 Service Pack 3 results in the Windows
NT blue screen. Microsoft has a post-SP3 hotfix available,
which is included in Service Pack 4. Contact Microsoft for
availability information.
C. Memory
More memory is required by ChemDraw when you increase the
number of colors available to greater than 256. To avoid memory
problems, increase the available memory (swap space) or decrease
the number of available colors. Refer to your Windows Help to
determine how to change these settings.
D. Fonts
The names of fonts stored in Style Sheets may not match
the names of the same fonts on international systems. In
this case, a strange font may result when you create a
caption or atom label. The solution is to select the desired
caption and label fonts on the international system, then
resave the Style Sheets (*.cds). See the user's guide for more
information.
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1. If you are experiencing strange display behavior, try changing your
display type to the standard VGA video driver that comes with
Windows. The display type can be changed using the Display
control panel. If this resolves your problem, contact the
manufacturer of your original video driver to see if there is an
updated version available.
2. Structures pasted into other applications may appear
larger or smaller than they do in ChemDraw. However,
printing occurs at 100% (if the application has a ruler
function, compare the relative size of an inch).
G. Printer drivers can cause problems.
If you are experiencing a printing problem, make sure you are
using the latest printer driver for your printer before contacting
technical support.
Windows NT: Certain printer drivers cause launching of
ChemDraw and opening of ChemDraw documents to take several
seconds.
Printer drivers may also cause problems upon application launch.
If you are having problems starting ChemDraw, try changing (or
removing) your default printer.
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H. Opening a file that is already open by another user gives
an incorrect alert. The incorrect alert reads "The file
could not be found".
-------------------------
IV. INFORMATION ABOUT CHEM3D 6.0
For that latest support information for Chem3D,
please see:
http://www.camsoft.com/support/topics.cfm?FID=3
A. New features in CS Chem3D Ultra 6.0
* New Computation Interfaces:
- GAMESS
- MOPAC 2000
- Gaussian 98
- MOS-F
- Tinker
* Property Broker
* ChemSAR
* Normal Mode Animation
* Improved Chem3D Plugin
* CIF File Format
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Please see the Chem3D User's Guide or Help Menu for more information
about these new features.
B. Video/Display Drivers
To get the best display results from Chem3D, use the most recent
drivers for your video card. Contact the manufacturer of your video
card for the most up-to-date drivers.
C. Memory
Take the following steps to reduce memory usage:
- Reduce the number of open model or table windows.
- Reduce the size of model windows.
- Avoid displaying Space Filling models while building.
- Do not record movie frames while doing minimizations or
rotations.
- If your model has more than one movie frame, use Edit/Clear
Frames/Clear All Other Frames to eliminate unneeded frames.
- If you have performed calculations, use Edit/Clear Calculations
to eliminate unneeded calculations.
- If you have created surfaces, use Edit/Clear Molecular Surfaces
to eliminate unneeded surfaces.
- In Movie Settings, reduce Smoothness (move the slider to the
right) to decrease the number of frames saved while
rotating.
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- Close Messages and Measurements windows when you no longer
need them.
- Close the Table Editor instead of leaving it in the
background or minimized on the desktop.
If you receive a warning that memory is low, save your work, exit,
restart Windows, and then restart the program.
D. Speed
If you find Chem3D to be slow during processing, take the following
steps:
- Simplify the display. Use Wire Frame or Ball and Stick model
types; choose Solid Colors instead of Shadowed.
- If you have a Messages or Measurements window open, clear its
contents: select the window, then choose Edit/Select All, Edit/Clear
- Close any windows you are not using.
- If the Table Editor is running in the background, close any
windows it has open or close the Table Editor and
run Chem3D only.
- If ChemDraw is running in the background, close it.
E. Colors
Chem3D supports a variety of model displays, shading schemes, and color
palettes. In some instances copying these structures out of Chem3D into
other programs will result in changes to the model displays. (reduced
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colors, banding, etc.) A majority of these cases are due to the other
program having a smaller number of colors than Chem3D available in
its program specific color palette. You either need to increase the
size of the program's color palette (if possible) or reduce the
number of colors used in the model.
F. PDB Files
If you experience problems opening PDB files, try to open
the PDB file with the Compute Atom Types and Bond Order options turned
on. You can access these options using the Option button on the Open
dialog box.
G. Cube Files
Chem3D supports only cube files containing the following data:
- charge density
- spin density
- molecular orbitals
- electrostatic potential
- difference density
Although Chem3D opens cube files containing other data, only molecule
data will be available. Surface data will not be available.
H. Users of Microsoft Plus! for Windows 95
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Chem3D will be able to display models better if you turn off the
Show window contents while dragging checkbox in the Plus! tab
of your Display settings.
I. Substructures
If you wish to create your own substructures for the
substructure table, use these settings to get your pictures to
match those already present:
Scale factor: 15/32 normal size
Model Type: Ball and Stick
Color by Element: On
Color by Depth: On
Atom Size: 16
Bond Width: 10
Depth Ratio: 75
J. Parameters
If you wish to create your own parameters for use in model building or
minimization, you can do so without altering the files provided. When
Chem3D loads parameters to create its internal tables, it reads all
files in the C3DTABLE directory and concatenates them together.
Therefore, you can create your own separate parameter files, place
them in the C3DTABLE directory, and have them automatically appended
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to the standard ones.
For example, suppose you have a set of MM2 atom types which apply to a
particular class of heterocycles. You can:
(a) Create your own small table of these parameters, and use it as a
supplement to the standard list. Using the Templates menu in the
Table Editor, select MM2ATYPE.TBT to open a new, empty table.
Use the Edit menu to create new records, and then fill in the data.
Save the completed file in the C3DTABLE directory, for example
with the name MYATYPES.TBL. Chem3D will then automatically use
this table in addition to the standard MM2ATYPE.TBL.
OR:
(b) Modify the existing set of parameters to include your own. In the
Table Editor, open MM2ATYPE.TBL, and use Save As to save a backup copy
in a directory other than C3DTABLE. Edit the table as desired,
modifying or deleting existing records and adding your own. Save the
edited file in the C3DTABLE directory with whatever name you choose.
Chem3D will use this table the next time it needs these parameters.
If there are conflicts --- multiple definitions of the same parameter
--- results are undefined. If you want to define your own value, be sure
to delete any existing one.
K. CS Gaussian Client
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The CS Gaussian Client is an add on module for CS Chem3D Ultra.
This client comes in two parts. The first part, called
CS Gaussian Client, is installed as part of CS Chem3D Ultra.
The second part, available from Gaussian, Inc. are the
Gaussian libraries that perform all of the Gaussian calculations.
For information about how to purchase the Gaussian libraries,
contact Gaussian, Inc. at http://www.gaussian.com.
With CS Chem3D Ultra, you can create Gaussian input files that
can be transferred to another computer to run the Gaussian calculation.
With the Gaussian libraries installed as well, you can do energy
minimizations, property calculations, and run input files from
other sources. Among the properties you can calculate are molecular
surfaces, such as molecular orbitals, total charge density surfaces,
spin density surfaces, and electrostatic potential surfaces.
The Gaussian libraries include the cubegen library. This library
is used by Chem3D to compute molecular surfaces from data that is
supplied by Gaussian.
CS Gaussian Client will automatically create output files for
each Gaussian calculation. These files are automatically written
to a subdirectory of your Windows directory. These files can
contain additional information about the calculation which
Chem3D may not be able to display. If you do not need these
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* ChemFinder for Word
* Form Security
* DAO
* Field Formatting
* Search subtables and main table simultaneously
* No limits on retrieved hits
* Hit list management
* Improved, standard OLE automation interface
* CAL Help
Please see the ChemFinder Manual or online help for more information
about these new features.
B. Samples
The Samples directory installed with the program contains
several small databases, forms, and sample scripts.
Notes:
The Cs_Demo database contains about 300 structures covering a
range of structural types. The database contains two tables,
both of which are visible using the form Cs_Demo.cfw. This is
the form used in the tutorials in the ChemFinder User's Guide.
Demo.cfw is a simpler form which displays only the main table
of the same database.
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We recommend you make a working copy of the database before
experimenting with it, because if you make changes to the
data or structures in that database, the examples in the
tutorials may no longer give the documented results. The
following procedure creates a working copy of the Cs_Demo.cfw
database.
To make a copy of the database:
1. Open Windows Explorer.
2. Select Cs_Demo.cfw, Cs_Demo.mdb, Cs_Demo.msi, Cs_Demo.mst,
right-click, and then choose Copy.
3. Deselect the files you selected in step 2.
4. Right-click and choose Paste. Copies of the files are added to
the directory.
You can now experiment with adding, modifying, and deleting
data in the copies with no effect on the Demo script or the Cs_Demo
database.
Other files of interest in the SAMPLES directory:
Sample.sdf: sample MDL-format Structure/Data File. Use
this to experiment with ChemFinder's Import SDFile feature.
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There are also files of interest in the ChemFinder System
directory. Any *.cfs file in this directory can be executed
from the Scripts menu. You can use a text editor to
look at _Demo.Cfs or Browse.cfs for examples of CAL programming.
ACX99INDEXA.CFW:
ChemCombi allows using data from chemical databases to serve as
input to its process.
However, ChemACX 5.0 has security which prevents a program
like ChemCombi from using ChemACX in this fashion. To correct this
ChemFinder 5.1 has included ACX99IndexA.cfw, in the samples directory,
as an alternate ChemACX form which allows this access.
It can be installed by copying it into the same directory as the
rest of the ChemACX files.
If you are using ChemACX from the CD-ROM, it isn't possible to copy
the file there. In that case it can left in the samples directory.
ChemFinder must be configured to allow the Acx99IndexA.cfw form to
find the ChemACX data.
If ChemACX 5.0 is installed on a hard drive:
Copy the \samples\ACX99IndexA.cfw into the
directory with the rest of the ChemACX 5.0 files.
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To use off CD or to leave the form in the samples directory:
In the [OPTIONS] section of the CFW.INI file add or edit the DB_SEARCH_PATH
key so that it points to the directory on the CD-ROM which contains
the ChemACX files. Make sure that if there are any previous paths
in DB_SEARCH_PATH, that they are seperated from this path by a semi-colon.
IMPORTANT NOTE: The path MUST end in a backslash. For example:
DB_SEARCH_PATH=D:\ChemACX\
Testing the setup:
To make sure you won't have any problems when loading the database from ChemCombi
test the database out by double clicking on the icon of Acx99IndexA.cfw from
the Windows Explorer, or start ChemFinder and use File->Open to load the form.
If the message "The database named in this formfile [
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2. Formulas for compounds containing carbon are sorted by increasing
C-H-N count followed alphabetically by any other elements.
D. Molecules with Multiply or Variably Attached Atom Labels
ChemFinder does not support importing of molecules with multiply
or variably attached points.
E. Multiple Users
ChemFinder databases may be used by several users simultaneously.
However, ChemFinder forms (.CFW files) may not. If you attempt
to open a form and get the message "Unable to open document," you
can (a) create a new form, (b) open a different form, or (c) use
File Manager or Explorer to make a copy of the form you are trying
to open; then use Database from the File menu to connect the form
to the target database.
F. Metafiles
Some older Windows metafiles may be opened and
displayed, but not copied or pasted from the Clipboard. More
recent ("enhanced") metafiles work better.
G. Stopping Searches
It is possible to abort a structure, formula,
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or molecular weight search by pressing ESC. It is not possible
to interrupt searches over other fields, since these searches
are carried out by the Access (or other ODBC) database engine.
H. Paradox (CISPro) Databases
Tables in a Paradox database, which is
the database used by CISPro, can be attached using the Attach Table
button in the Database tab of the properties dialog like other
non-Accessformat files. However there are two problems when using
this data:
- Searches are case sensitive.
- When a search is performed in some fields doing a Search->Find
brings up the following message: "'#Temporary QueryDef#' isn't
an index in this table. Look in the Indexes collection of the
TableDef object to determine the valid index names." Microsoft
Access also gives the same error. Its possibly a corrupt
database or perhaps the Microsoft Jet engine doesn't interact
well with Paradox indexes. This issue is under investigation.
I. Older installations
If you have ChemFinder 4.x or earlier already installed,
installing this version of ChemFinder will not overwrite
the earlier one. The older version will be in a folder named
ChemFindr; the new one will be in the folder named ChemFinder in
the ChemOffice directory. Be sure to move any custom scripts and
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databases from the ChemFindr folder into the appropriate locations
in the ChemFinder folder before deleting the older folder.
J. Visual Basic Automation Change
You must now declare a Molecule object as As Object. Declaring
a molecule as ChemFinder.Molecule is no longer supported. Visual
Basic client applications being served by ChemFinder will no
longer compile if they contain codedeclaring a molecule this
way. For a molecule named Mol:
Dim Mol As Object // Correct
Dim Mol As ChemFinder.Molecule // Incorrect, not supported
K. ChemFinder for Excel
ChemFinder for Excel is not compatible with any version of ChemDraw
before 5.0 nor is it compatible with ChemDraw 5.0 Net. If
ChemDraw Net was installed as the last version of ChemDraw, then
ChemFinder for Excel will present a message saying that
ChemDraw Std 5.0 or greater is required. Installing a higher
level of ChemDraw, such as ChemDraw Pro will fix the problem.
If ChemDraw hasn't been installed at all, double clicking in a
ChemFinder for Excel worksheet will present an error dialog. You can
still input molecules into a ChemFinder for Excel worksheet without
ChemDraw installed by importing a .SDF file, importing a ChemFinder
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database, using the Get ChemFinder List command or the Convert SMILES
to Molecule command.
-------------------------
VI. UNINSTALLING CAMBRIDGESOFT PRODUCTS
To uninstall any CambridgeSoft Products:
Personal stationery and templates may exist in your CD_Items
directory. You should make a backup of these files so that you
can reinstall them at a later time. You should also move any
personal ChemDraw documents you have created to a temporary folder
on your hard drive.
From the Start Menu, Choose Control Panels from the Settings
submenu. Choose Add/Remove Programs. Choose the CambridgeSoft
(CS) product you wish to uninstall. Click the Remove Button.
This will launch the uninstall program.
If the CambridgeSoft product is not listed in the Add/Remove
Programs Control panel, (A) look in the ChemOffice Program
group for an Uninstall Program, or (B) if no uninstall program
can be found, delete the entire ChemOffice or ChemDraw directory.
Depending on which CambridgeSoft product you have installed, you
may have any of the following files still remaining in your
Windows (or WinNT) folder:
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c3dprefs.dat
chem3d.ini
chemdraw.ini
cfw.ini
CSMopac.ini
CSGaussian.ini
-------------------------
VII. SOFTWARE DEVELOPMENT KIT
Documentation for OLE Automation and more information about our
Software Development Kit can be found at:
http://sdk.camsoft.com
-------------------------
VIII. TECHNICAL SUPPORT
See the Technical Support web site for solutions to the
most common problems: http://www.camsoft.com/support/
To report bugs or ask questions, please use one of the following
addresses. We recommend using the web submission form, since
this form asks for the detailed information we most often need
to help solve your problem.
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Web Submission Form:
http://www.camsoft.com/support/suppProbRep.cfm
E-mail: [email protected]
Post: Technical Support Staff
CambridgeSoft Corporation
100 CambridgePark Drive
Cambridge, MA 02140
Fax: 1 617 588-9360