Isis Draw For Mac |WORK|
ISIS/Draw was a chemical structure drawing program developed by MDL Information Systems. It introduced a number of file formats for the storage of chemical information that have become industry standards.
Isis Draw For Mac
MDL introduced specifications for chemical file formats, including the molfile (.mol), and structure/data file (.sdf) which were subsequently placed in the public domain and have become standards for representing structures in 2-D drawings and for transferring such information with associated data, for example identifiers, chemical names and substance properties.Many public databases implemented these standards and ChemSpider, for example, allows users to download molfiles for the structures it holds. ISIS/Draw retained its own proprietary file formats with the extension .skc (sketch file) and .rxn (for reactions) and because of its role in preparing database queries it supported a variety of special atom and bond types used for substructure searching, such as wildcard atoms, aromatic bonds, ring bonds, and the atom mapping required for reaction searches.
While ISIS/Draw was mainly a 2D drawing program, it had some 3D rotation features and could interface with Rasmol for 3D visualization and rendering. ISIS/Draw also included structure and reaction validation features and could calculate elementary properties such as formula and molecular weight. It had an "AutoNom" add-in that allowed the creation of IUPAC names for valid structures and could use a special "pseudoatom" to generate amino-acid sequences for proteins.
The current (2020) implementation of the software is called BIOVIA Draw and has several new features such as support for reading and writing International Chemical Identifiers (InChi) and converting IUPAC names into structure drawings. It is freely available for academic and non-commercial use.
GeneralThe ISIS collection of databases contains over 700,000 reactions. Althoughthis is quite a lot, it is nowhere near comprehensive. It is good to use ifyou want to search for a type of reaction without being too specific aboutthe exact substituents. The advantage over Beilstein is thatsearching is usually quite a lot faster. A Tutorial is available.Userids should be obtained by registering on-line at are available to everyone working in UK academic institutions. The required software can all be downloaded once youhave registered.The ISIS/Base program in the Silicon Graphics Teaching Lab is an earlierversion than that available for PCs and Macs. The instructions for theearlier version (in the SGTL) are provided below followed by thedifferences in the later PC and Mac versions.Performing a Search in the Silicon Graphics Teaching LabThe following is a set of instructions for performing a simple reactionsearch using ISIS. You will see that there are a great many features of theISIS/Base program that are not described. Extensive Help files can beaccessed from within the program and should be sufficient for anyone whowants to know more.To run ISIS/Base and access the Daresbury database, enter the command"isis". (The command"mdlbase /usr/local/mdl/all.db"which used to be recommended will still work.)Enter your Username in the box. EnterPassword in the next box that opens.The "Reaction Form" should open with the "Query" box highlighted at thetop. Double click on the main window. This opens ISIS/Draw for drawingstructures.Fig. 1 The ISIS/Draw window as it appears once a reaction has beendefined. Draw the starting material(s) to the left and/or the product(s) to theright. Draw in H atoms at any site where you don't want to allow anysubstitution but leave them out if you want to allow any substituent atthat site.Select the tool which is an arrowhead surrounded by a square of dots. Clickon the first molecule and then, while holding the shift key down, on theother molecules also. Each should get a square of dots around it and aletter beneath. Select "Reaction..." from the "Chem" menu. In the windowwhich opens click on the box where the arrow should be and then click OK.Fig. 1. shows how the screen should appear.Click on the ISIS Base icon at the top of the tool strip (below File menu)to return to ISIS Base. The reaction you drew should be in the main box.Under "Search" menu click on "Automap Rxn" and then on "By Form" or "RSS"(for Reaction Substructure Search).When the search is complete, the form will indicate just below the menu barhow many hits have been found and will enter "Browse" mode in order to viewthe hits. To move from one hit to the next click the up arrow or down arrowon the left of the window. Alternatively click on "#" and enter the hitnumber you want. The window should look like the following:Fig. 2 The ISIS/Base window showing one hit from a search.To modify the search, click on "Query" mode, double click on the reactionwindowand edit the reaction in ISIS Draw. Then repeat the search as above.On Mac or PCDouble click on the ISIS/Base icon to start the program then choose "OpenDatabase" from the "File" menu and double click on "rxl13.db" for PC or"RXN Browser" (may be in RXN Browser folder) for Mac (or maybe "RXL Browser").It may be thatISIS/Draw needs to be opened manually by double-clicking on its icon beforedouble-clicking on the "Paste Reaction" box to switch from ISIS/Base toISIS/Draw.If the latest versions of ISIS Base (2.x.x), ISIS Draw and RXN Browser areinstalled,you will find they are a bit different from that described above:1. The first window when you open "RXN Browser" offers the choice ofan "Expert Query form" or a "Query Assistant" (see Figs 4 and 5 below).Generally use "Query Assistant". In the next screen click on "Substructure"(i.e. partial structure) or "Full structure" (i.e. exact structure) forreactant and product. Then click on "OK". In the next window double clickon the main box to run ISIS/Draw in order to draw the desired reaction.2. In ISIS Draw the main difference is in defining the reaction(i.e. which molecule is the reactant and which the product). To do this youselect the Arrow tool and draw an arrow in the appropriate place on thescreen. If there is more than one reactant select the "+" tool and place a+ in the appropriate place. To cleck that this will be interpretedcorrectly click on the icon which shows a tick in the middle of a hexagon(or select "Chem Check" from the "Chemistry" menu). See below, Fig. 3 for apicture of the screen along with instructions.Fig. 3 The ISIS/Draw 2.1.3 window on a Mac, withinstructions.3. To transfer the reaction you have drawn in ISIS/Draw into the"Paste Reaction" box of ISIS/Base click on the ISIS/Base icon at thetop-left corner of the ISIS/Draw screen (just above the lasso icon). Youshould now see an ISIS/Base window similar to Fig. 4 (Advanced Query) orFig. 5 (Query Assistant).Check that the correct search type has been set. The alternatives are"Current Reaction" (i.e. exactly as drawn), "Reaction Substructure", "SameTransformation", and "Similarity". "Automatic Search" does all of these oneafter the other and so generates the greatest number of hits.Automapping is normally done automatically but if this is not the case itcan be applied by clicking on "Automap" in the top row of buttons in theISIS/Base window. Run the search by clicking on "Search" (the right-hand button in the toprow).Fig. 4 The ISIS/Base Advanced Query Window on a Mac.Fig. 5 The ISIS/Base Query Assistant Window on a Mac.4. When browsing through the hits the window is different from theQuery mode one (see Fig. 6 below). There are different forms available,which display different selections of information. These can be selected byclicking on the boxes "Summary", "Reference"..."Table" at the top of theform. The "Table" form gives a number of hits, one below the other, and isa quick way of looking through the hits.Fig. 6 The ISIS/Base Browse Hits WindowOlder versions for Mac or PC2. In older versions of "RXN Browser" the Reaction Form was ratherdifferent (see below)but for simple searches you still only need to use the "Paste Reaction"box. Automapping is normally done automatically but if this is not the caseit can be applied by clicking on "Automap" just above the top right cornerof "Paste Reaction" box. Run the search by choosing "ByForm" or "RSS" or "Exact Search" from the "Search" menu.Fig. 7 Older version of the ISIS/Base Query Window on a PC, withinstructions on its use.The window for browsing through the hits was also different in earlierversions. The different forms available, which displaydifferent selections of information, can be selected by clicking onthe boxes "d1", "d2"..."cl" on the left of the window. The "cl" form isoften the default and behaves a bit differently: when it is selected thehits are clustered according to some criterion of similarity; to move fromone hit to the next within a cluster click on the up and down arrows at theleft of the window but to move to the next cluster click on the "NextCluster" box above the reaction display box.Other Databases at DaresburyThe Chemical Database Service at Daresbury also has databases forcommercially available chemicals (ACD), protecting groups (SPG), separationof enantiomers (Chirbase) and, for a trial period, solid phase synthesis(SPS) and solid phase organic reactions (SPORE). These are all accessed viaISIS/Base using different browsers. The "ACD Finder" browser is installedon the PWF.For further details click here. Goodman Group, 2005-2023; privacy; last updated January 28, 2023
ChemSketch is a program that allows you to draw organic chemical structures. The drawings can be used as (2D) structures, for example in word processing files, or they can be converted to 3D models. I have posted an introductory guide for this free program; the guide tells you how to get the program, and then helps you get started using it. Introductory guide: ChemSketch
RasMol is a classic program for viewing 3D molecular structures. You can also perform a variety of manipulations on them. Using RasMol is something like using a box of models, but lets you view much larger molecules. Thousands of "pdb" files are available, for small molecules and for macromolecules, for RasMol. (Some of the newer programs for viewing molecular structures use code or ideas from RasMol.) I have posted an introductory guide for this free program. It tells you how to get RasMol, introduces you to using it, and provides some sources of structures that you can view. It explains how to make your own 3D structure files, using the drawing programs listed above. It also contains some suggestions keyed to my X402 course, Introduction to Organic and Biochemistry. My Introductory guide for RasMol.