2/14/94 ==> README File for ISIS/Draw version 1.2W (Microsoft Windows) <== (c) 1994 MDL Information Systems, Inc. All rights reserved. THE USE OF THIS SOFTWARE IS GOVERNED BY THE TERMS AND CONDITIONS DESCRIBED IN THE FILE LICENSE.TXT This document provides information about the following topics: 1. How to contact MDL 2. Changes to the installation procedure 3. Known limitations of ISIS/Draw version 1.2W 4. Compatibility with other Microsoft Windows Applications 5. Documentation additions 6. Documentation corrections 1. HOW TO CONTACT MDL For more information on MDL products, see the MDL Home Page at URL: http://www.mdli.com Also you can subscribe to the ISIS discussion group listserver by sending an E-mail to mailserv@mdli.com with a single line message as follows: subscribe isisforum-l ------------------------------------------------------------------------ 2. CHANGES TO THE INSTALLATION PROCEDURE There are no changes to the installation procedure. ------------------------------------------------------------------------ 3. KNOWN LIMITATIONS OF ISIS/DRAW VERSION 1.2W a) Extended Periodic Table (PTable) in ISIS/Draw Differs from Other MDL Products The amino acids in the extended periodic table (PTable) in ISIS/Draw differ from the amino acids in the extended periodic table that is supplied with MACCS-II and REACCS. If you import structures from MACCS-II or REACCS that contain amino acids from a customized Ptable, ISIS/Draw cannot interpret these atoms correctly. (CW-10473) b) Text Copied with Reaction Might Be Positioned Incorrectly When you transfer a reaction from ISIS/Draw to ISIS/Base, text objects adjacent to the reaction components might not be positioned correctly in ISIS/Base. This applies to reactions that are pasted from the clipboard and to reactions that are transferred with the Transfer button. (CW-10637) c) Structures Grouped With Sketch Objects Are Not Chemically Significant Do not group chemical structures or reactions with sketch objects. If you do, ISIS/Draw interprets the structure as a sketch object and the structure loses all chemical significance. Also you cannot export the structure to a molfile (reaction to a rxnfile) or copy it to the Clipboard as a CTfile. (CW-08708) d) ISIS/Draw Imports *STEXT From CPSS Molfiles ISIS/Draw will import *STEXT from a CPSS molfile to save in a sketch. However, you cannot export *STEXT to an ISIS/Draw molfile. (CW-06034) e) ISIS/Draw Does Not Support Substance Module Features ISIS/Draw does not support substance module features. Therefore, you cannot import or export molfiles with structures that contain superatoms. ISIS/Draw will display an error message. (CW-08021) f) Molecule Clean Does Not Scale Atom Labels When you select a molecule with the Component tool, and then choose Clean from the Chem menu, the bond length and angles are adjusted, but not the size of the Atom Labels. To adjust the size of the atom labels, select the molecule with the Component tool, and then choose a new size from the Style menu (shift-click with the Select tool to select individual atoms to restyle). (CW-08186) g) Style Menu Will Not Display Checkmarks With Multiple Objects Selected If you select a combination of objects, for example atoms and bonds, and pull down the Style menu, you do not see any checkmarks. ISIS/Draw does not show the checkmarks, because it is possible that each object has a different combination of styles applied. (CW-08478) h) Transferring Macintosh Files to the PC To export a TGF file, molfile, or rxnfile from the Macintosh to the PC, press and hold down the Option key while you highlight Export on the File menu, and choose either TGF, Molfile, or Rxnfile from the cascading menu. Next, always use the Text Translation setting in the Apple File Exchange to transfer these Macintosh files to the PC format. Activate the Replace CR with CR/LF check box, and set the Special Characters and Tab Characters radio buttons to Neither. DO NOT USE THE DEFAULT TRANSLATION SETTING. (CW-03963) ------------------------------------------------------------------------ 4. COMPATIBILITY WITH OTHER MICROSOFT WINDOWS APPLICATIONS a) CorelDraw Objects are Incomplete When They are Inserted Into ISIS/Draw In ISIS/Draw, if you choose Insert Object from the Edit menu, and then choose CorelDraw to create an object, when you return to ISIS/Draw only part of the object appears. The same object appears incomplete when it is inserted into other applications, such as Microsoft Word. (CW-05875) b) WordPerfect for Windows Printer Drivers To provide better printing of text in ISIS/Draw sketches from within WordPerfect, change the WordPerfect printer driver to the Windows printer driver before you print. In WordPerfect, choose Select Printer... from the File menu. Select Windows from the Printer Drivers options. Click Select (do not click Close). You might also have to resize objects in WordPerfect as close as possible to their original size before you print them. This will help to prevent the text from overlapping. (CW-08219) ------------------------------------------------------------------------- 5. DOCUMENTATION ADDITIONS a) Changing the Default Font for Text To change a default font so that it becomes the new default, click the Select tool. Click in a blank area in the drawing area to make sure that you do not have any text selected. Choose a new font and font size from the Style menu. To make the change the default for future ISIS/Draw sessions, choose Preferences... from the Options menu. Click Save to update the ISIS/Draw configuration file (ISISDRAW.CFG). Click OK. b) Changing the Default Styles for Objects (Pen Width, Color, Line Styles) To change a default style so that it becomes the new default, do NOT select any objects in your sketch before you choose the new style from the Style menu. The style choice becomes the new default for the current session that will be applied to other new objects in your sketch. (To save the default for future sessions, choose Preferences... from the Options menu, and then click Save.) To change the style of an existing object with out changing the default Style, select the object before you choose a new style from the Style menu. c) Preference Affects How Text Displays and Prints in Sketches When the "Adjust text display to match printed appearance preference is active (the default), you can add or modify text in your sketches using the same font size width that your printer uses. This is very helpful when you add text to sketch objects, such as boxes, because if the text on screen does not overlap the sketch object boundaries, then it will not do so when it is printed. However, there are differences between the Windows screen and printer fonts that might cause the adjacent characters in text to overlap or display uneven spaces. When you are done drawing and saving a sketch, you can inactivate the "Adjust text display to match printed appearance" to improve the resolution of the font display on screen. See page 6-12 of the "ISIS/Draw Installation & New Features" manual for more information. d) Adding Atom Subscripts There are two methods in which you can add subscripts to atoms in ISIS/Draw: o Select an atom with the Select tool (or click in a blank area in the drawing area, and then enter an atom symbol, followed by the number you want to subscript. Press RETURN. o Click the Text tool and enter an atom symbol. Press the Ctrl and - (minus) keys simultaneously to activate subscripting. Enter the number you want to subscript. Press the Ctrl and the + (plus) keys twice simultaneously to turn the subscripting off. NOTE: On European keyboards, you must use the + and - keys located on the numeric keypad instead of on the top row of your keyboard. The two methods to create an atom subscript will look different when printed. We recommend the first method, because the subscript appears smaller and with less white space surrounding the subscript. (CW-08903) e) Superscripting Text From the Keyboard As you type text (with Text tool), you can turn superscripting on and off. To do so, press the Ctrl and the + (plus) keys simultaneously. Text that you type is superscripted. To turn the superscripting off, press the Ctrl and the - (minus) keys twice simultaneously. NOTE: On European keyboards, you must use the + and - keys located on the numeric keypad instead of on the top row of your keyboard. (CW-09278) f) Using a Font Translation File For TGF File Transfers If you often import TGF files created on the Macintosh, you can create a font translation file on the PC that can be used to translate font differences between the PC and Macintosh. Create an ASCII file called ISISFONT.DAT in your Windows subdirectory. The file should list, line-by-line, all of the commonly used font names for sketches on the PC, followed by an equal sign, followed by the names of the Macintosh fonts that you want to use as substitutes. For example: pcfontname1=macsubstitutefont1 (<---this could be Arial=Helvetica) pcfontname2=macsubstitutefont2 . . . ISIS/Draw will read the ISISFONT.DAT file upon importing TGF files. Note: The TGF file supports the transfer of extended ASCII characters that exist on both platforms. --------------------------------------------------------------------------- 6. DOCUMENTATION CORRECTIONS a) Displaying Hydrogen Atoms The procedure "To display all terminal hydrogen atoms" on pages 2-23 and 2-24, and the "Hydrogens" reference on page 12-12 should be updated to reflect a change in hydrogen display in ISIS/Draw. Select individual atoms or whole structures to display or hide hydrogens on terminal carbon atoms and all heteroatoms or on non-carbon atoms only. Choose Hydrogens from the Chem menu, and you have the following options: o Choose On to show hydrogen atoms for terminal carbon atoms and all heteroatoms o Choose Off to hide hydrogen atoms o Choose Hetero to display hydrogens on non-carbon atoms only Also, when you choose to display hydrogens below or above an atom, the number moves to the side of the hydrogen rather than below or above it. For instructions on how to position hydrogens, see "To display specific hydrogen atoms" on page 2-23 of the "ISIS/Draw Reference" manual. b) Using the Grid to Draw Structures Atoms in templates will no longer snap to the grid. This will prevent templates, such as cyclopentane, from distorting if you are using a hexagonal grid. This information updates the procedure "To draw rings on the grid" on page 2-61 of the "ISIS/Draw Reference" manual.