12.6 ISIS/Draw - 2D molecular editor

12.6.1 Introduction

ISIS/Draw is a well know two dimensional molecular editor mainly used to put structures in databases and/or in documents. The plug-in allows to edit molecules already present in the current VEGA ZZ workspace transferring them to the ISIS/Draw environment. The modified structures are automatically re-transferred to the VEGA ZZ workspace updating the previous structures. If required, the structures generated by ISIS/Draw can be converted from 2D to 3D by AMMP molecular mechanics engine.

12.6.2 Requirements

The plug-in works properly only if the ISIS/Draw 2.5 is correctly installed. The advanced technique to control the ISIS/Draw application (called code injection) is available in Windows versions with NT kernel only (Windows NT 4, 2000, XP, Server 2003, Vista, Server 2008 and 7).

12.6.3 ISIS/Draw 2.5 installation

• The package is free available for academic non-profit use after the registration procedure. Please remember that the plug-in supports the 2.5 english release only. Other releases and the kanji version are incompatible.
• Run the setup.
• At the end, restart the PC. If you skip this step, the VEGA ZZ is unable to start properly ISIS/Draw.

12.6.3 Usage

To start ISIS/Draw, you must select Edit ISIS/Draw in main menu. If you start ISIS/Draw from the Windows start menu, the communication with VEGA ZZ is not operative.
If a molecule is present in the current workspace, it will be transferred automatically to the ISIS/Draw environment, otherwise a blank project is created.

To transfer the molecule to VEGA ZZ, you can proceed in two ways:

• Close the ISIS/Draw window: a message box is shown asking if you want update VEGA ZZ before exit. You can select Yes to update VEGA ZZ and close ISIS/Draw or No to close ISIS/Draw without the update and Cancel to abort the procedure.
• Select the custom menu VEGA ZZ Send to VEGA.

If the VEGA ZZ Convert to 3D menu item is checked, the structure is automatically converted to 3D during the transfer, following these steps:

• Add the missing hydrogens. This operation is executed only if no hydrogens are present. To force this step even if the hydrogens are already added, you must check the VEGA ZZ Force add hydrog. menu item.
• Distance geometry optimization with the Gauss-Siedel algorithm (15 steps).
• Steepest descent minimization (50 steps, toler = 1.00) .
• Conjugate gradients minimization (3000 steps, toler = 0.01).

12.6.4 Configuration file

...\VEGA ZZ\Plugins\plugins.ini file contains the start-up configuration of all plug-ins. The [ISIS/Draw] section allows to change the default parameters used by the ISIS/Draw plug-in. Each line is a parameter in the format:

PARAMETER_NAME = VALUE

The following table shows all parameters that you can change in the configuration file:

Plugin.ini section example:

[ISIS/Draw]
CONVERT_TO_3D=1
FORCE_ADD_H=0
GSDG_STEPS=15
STEEP_STEPS=50
STEEP_TOLER=1.00
CONJ_STEPS=3000
CONJ_TOLER=0.01

WARNING:
[ISIS/Draw] section could be not present in the configuration file until the plug-in didn't save them. To force it, you must open ISIS/Draw inside VEGA ZZ, change the configuration (e.g. checking and unchecking the Force add hydrog. menu) and closing ISIS/Draw.

12.6.5 Limits

Due to the MDL mol file format limitation, molecule with more than 999 atoms aren't editable.
When you transfer a 3D structure to the 2D ISIS/Draw environment, it could be difficult to edit the molecule because some atoms could be overlapped.

12.6.6 Copyright

ISIS/Draw 2.5
Copyright 1990-2023, Elsevier MDL
2440 Camino Ramon, Suite 300
San Ramon, CA 94583
Tel: +1 (925) 543-5400
Fax: +1 (925) 543-5401
E-Mail: info@mdl.com
WWW: www.mdli.com