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

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