README
======

Contents
--------
1.   New features in HyperChem Release 4.
     
       3-D tool icons and dialog boxes
       Pop up help for tool icons
       Faster calculations
       Network licensing
       Remote calculations
       New script & DDE messages
       Print dialog box
       Element table dialog box
       Command line arguments
       Additional Extended Huckel parameters
       AMBER parameter set from ChemPlus

2.   Corrections to the documentation.
     
       Reference Manual

3.   Hints on particular aspects of the use of HyperChem.
     
       Joining the HyperChem e-mail users group
       Saving vibrational and UV-visible spectra
       Recursive scripts
       Speeding up DDE Executes to HyperChem
       Altering chem.ini settings

4.   Notes on specific printers and display devices
     
       Changes for an IBM 8514/a display adapter or compatible
          display card
       Printing to the Apple Laser Writer IINTX:


1.   New features in HyperChem Release 4.
=========================================

3-D tool icons and dialog boxes
-------------------------------

HyperChem now has tool icons and dialog boxes with a gray, 3-D
appearance.  The tool icon that is active appears depressed, giving
visual feedback on which tool is currently active even when the mouse
cursor is outside the HyperChem workspace.  This feature can be
disabled by setting Look3D to No in your chem.ini file.

Important: For the 3-D appearance of dialog boxes, HyperChem uses a
shared system file (redistributed from Microsoft) called CTL3D.DLL.
In order to avoid possible conflicts with a previously installed
CTL3D.DLL that may already be in use by Windows, the HyperChem setup
program copies this to the same directory as the HyperChem executable
files.  You should move CTL3D.DLL to your Windows SYSTEM directory
unless you already have a newer or the same version of CTL3D.DLL
there.  Once the newest version of CTL3D.DLL is in your Windows
SYSTEM directory you should delete or rename the copy in the
directory with HyperChem executable files.  Display problems may
occur if you leave an older version of CTL3D.DLL in your Windows
SYSTEM directory.

Pop up help for tool icons
--------------------------

If the mouse cursor pauses for a few seconds over one of the tool
icons, a short message will now pop up to remind you of the function
of the tool.  You can disable this feature by setting ToolHelpPopup
to No in your chem.ini file.

Faster calculations
-------------------

The molecular mechanics calculations have been sped up typically by
10 to 20% and semi-empirical calculations have been sped up by 30 to
200%.  The greatest speed improvements have been obtained for AM1 and
PM3 calculations.  In addition, the molecular mechanics and semi-
empirical modules are now optimized for Pentium processors (without
slowing processing on 486 computers).

Network licensing
-----------------

HyperChem now offers network licensing for NetBIOS, IPX/SPX and NDIS
networks including Windows for Workgroups, LAN Manager, and Novell
Netware.  If you have purchased a network version of HyperChem, once
you have correctly installed the hardware lock on one PC, all
compatible PCs on the network can be set up to run HyperChem.  The
number of HyperChem sessions that can be run simultaneously is
limited to the number of licenses that you have purchased, unless you
have purchased the unlimited license version.

Caution:  HyperChem first tries to locate a local non-network lock
and if none is found it then tries to locate a network lock.
Locating a network lock may take a noticeable amount of time.  If you
use an older, unsupported network and HyperChem does not find a local
lock, it may interfere with the network software on your PC.  If you
use a non-network lock, you should ensure that it is properly
installed before you try to run HyperChem.

Remote calculations
-------------------

Instead of using the processor of your PC for time consuming
molecular mechanics and semi-empirical calculations, you can instruct
HyperChem to perform those calculations on more powerful computers
running the UNIX operating system.  Your PC must be connected to the
UNIX computer via a network, your PC must be running network software
that supports the Windows Socket (WINSOCK) 1.1 standard, and you must
have purchased and installed HyperChem remote backend modules for the
UNIX computer.

New script & DDE messages
-------------------------

The following HyperChem messages have been added:

          print
          is-ring-atom
          is-extended-hydrogen
          atomic-symbol
          atom-color
          atom-label-text
          residue-count
          serial-number

See on-line help or the Reference manual for descriptions of these
messages.  See the Corrections to the documentation section below
for descriptions of the print, residue-count and serial-number
HyperChem messages that are missing from the Reference manual.


Print dialog box
----------------

The HyperChem File/Print menu item now brings up the standard Windows
3.1 Print dialog box which allows you to choose a printer and set
printing options before starting to print.  The menu-file-print
script command now invokes the Print dialog box.  The print script
command has been added to print without invoking this dialog box.

Element Table dialog box
------------------------

The Element Table dialog box no longer returns the focus to the
HyperChem workspace but you can begin drawing immediately in the
HyperChem workspace after choosing an element.  The currently chosen
element is shown with a depressed button.  The tool is automatically
changed to the drawing tool.  You can also now choose an element and
dismiss the dialog box by double clicking on the element.

Command line arguments
----------------------

HyperChem now takes command line arguments and sets up Windows to
start HyperChem with a file when you click on that file name in File
Manager, provided the file has one of the extensions HIN, ENT or SCR.
If the extension is HIN, HyperChem tries to read the file as a HIN
file.  If the extension is ENT, HyperChem tries to read it as a file
in Brookhaven Protein Data Bank format.  If the extension is SCR,
HyperChem assumes that the file contains HyperChem script messages
and tries to run it as a script file.

Additional Extended Huckel parameters
-------------------------------------

Parameters for additional elements have been added for the Extended
Huckel method.  The following elements now have parameters:  K, Ca,
Sc, Zn, Ga, As, Se, Br, Rb, Sr, Zr, In, Sn, and Te.  These were
obtained from a compilation of published parameters collected by
Santiago Alvarez, Barcelona, September 1985.

AMBER parameter set from ChemPlus
---------------------------------

An additional AMBER parameter set for polysaccharides, called AMBERS,
is included for compatibility with ChemPlus.  This parameter set is
used with the Sugar Builder in ChemPlus, and adds some new types and
parameters to the AMBER3 set. It is taken from S. W. Homans, Biochemistry,
29:9110, 1990.  The HyperChem type rules are not changed, so these
types are not automatically assigned by HyperChem; you should
purchase ChemPlus if you wish to use this parameter set with
polysaccharides.

Caution:  If you install ChemPlus after installing HyperChem
Release 4, you should choose to not have ChemPlus installation update
HyperChem files.  If you allow ChemPlus installation to update
HyperChem files you will end up with duplicate saccharide residue
descriptions in the CHEM.TPL file that you can remove with a text
editor.


2.   Corrections to the documentation
=====================================

Reference Manual
----------------

On page 187 of the Reference Manual, in the periodic table showing
available parameters for Extended Huckel, the following elements
should be shaded:

 K, Ca, Sc, Zn, Ga, As, Se, Br, Rb, Sr, Zr, In, Sn, Te

The following HyperChem messages do not appear in Chapter 10 of the
Reference manual (but are included in the on-line help for
Scripts & DDE):

Script Command:     print
Arguments:          none
Use:                Prints an image of the system using the default printer
                    and print options.

Script Variable:    residue-count
Type:               int1, int2
Read/Write Status:  R
Use:                If you give the molecule number (int1), reports the
                    number of residues (int2) in this molecule.

Script Variable:    serial-number
Type:               string
Read/Write Status:  R
Use:                The serial number of the copy of HyperChem in use.

On page 291, the menu-file-print file menu activator should have
Print as the dialog box.

On page 331, the description for serial-number should appear instead
of the duplicate description of version.


3.   Hints on using specific aspects of HyperChem.
==================================================

Joining the HyperChem Internet e-mail users' group
--------------------------------------------------

The HyperChem Internet e-mail users' group is designed to encourage
users to share their experiences and ideas to improve their use of
HyperChem.  Information on scientific and technical issues, such as
Visual Basic tools, HyperChem structures, and product support
questions, can be posted to this group.  To become a subscriber, send
an e-mail message to:

 hyperchem-request@hyper.com

with the line:

 subscribe hyperchem

as the message body.  You will automatically be subscribed and sent
instructions on use of the e-mail group.

Saving vibrational and electronic spectra
-----------------------------------------

The HyperChem sample files include script files for saving HyperChem
vibrational and electronic spectra results so that you can read them
back into HyperChem for later use.  These scripts cause HyperChem to
create new script files that can be opened later to restore the
results.  The sample files are called SAVEIR.SCR and SAVEUV.SCR (for
vibrational and electronic results respectively).  See the comments
within these files for further details.

Recursive scripts
-----------------

From a script that you write with a text editor, you can call another
script (called recursive scripting).  The recursion depth depends on
finite system resources, however, and will thus vary depending on the
scripts and available resources.

Speeding up DDE Executes to HyperChem
-------------------------------------

The speed of DDE Execute commands that alter properties of molecules
in HyperChem can be sped up by using the "inhibit-redisplay" script
command.  Turning redisplay off (inhibit-redisplay Yes) before
sending a set of Execute commands to HyperChem, and then turning
redisplay on (inhibit-redisplay No) after they are complete speeds up
the execution.  You should be aware that if inhibit-redisplay is left
in the "Yes" state the HyperChem workspace will not be updated at all
until the inhibition is removed by executing an "inhibit-redisplay No"
command.

Altering chem.ini settings
--------------------------

If you wish to alter chem.ini settings that are not accessible
through the user interface, such as QuantumPrintLevel and
MechanicsPrintLevel, you can follow one of the following two
procedures.

     Edit chem.ini
     -------------
a. Close all copies of HyperChem you may have running, as HyperChem
   writes over chem.ini on exit.

b. Edit the file chem.ini with a text editor, such as Notepad, and
   alter the settings you wish to change.
   
c. Start HyperChem; the new values of chem.ini settings will be read
   in and used.
   
     Reset from a script
     -------------------
This method has the advantage that you do not have to exit HyperChem
to change the settings.

a. Write a script containing a command that resets the desired
   setting.
   
b. Run this script from the Script menu.  The desired setting is
   altered immediately.
   

4.   Notes on specific printers and display devices
===================================================

Changes for an IBM 8514/a display adapter or compatible display card
--------------------------------------------------------------------

If you are using an IBM 8514/A display adapter or compatible such as
the ATI Ultra Display video card, you may notice a number of random
scan lines at the bottom of your HyperChem window.  To remedy this
situation, exit HyperChem and open the chem.ini file with a text
editor such as Write or Notepad (don't convert to Write format).
Under the heading [HyperChem], type the following: SlowErase=Yes.
The next time you initiate HyperChem, the chem.ini file with it's new
addition will be read.  SlowErase will clean up your display, but you
will experience a 50% decrease in painting speed.  If speed is more
important to you than noise, you can delete the SlowErase entry from
chem.ini, or set SlowErase=No.

Printing to the Apple Laser Writer IINTX:
-----------------------------------------

If you experience problems with default settings when you send large
batch jobs to the postscript printer, try using the following
settings:

     In the Connect Dialog Box:
          Transmission Retry   500
          Fast Printing Direct to Port = deselect
     In the Settings Dialog Box:
          Baud rate  = 9600
          Data bits  =  8
          Parity   = None
          Stop Bits  = 1
          Flow Control   = Hardware
     In the Setup/Options Dialog Box:
          Send Header with Each Job  = deselect
     In the Advanced Options Dialog Box:
          Use Printer Fonts for all True Type Fonts  = deselect
          Virtual Memory (KB) (Tested at 2048KB)  = max. avail (print
          testps.txt to check value).
          Compress Bitmaps  = deselect
          Conform to Adobe Document Structuring Convention = deselect
     Return to the Options Dialog Box:
          Send Header   = select
          Send Header with Each Job = deselect .

