Molecular Modeling for EducatorsÔ
Opening and Saving Molecules
Version 5.2
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Molecular Modeling for EducatorsÔ |
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Opening and Saving Molecules |
Version 5.2 |
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MDL Molfile (.mol) |
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MACROMODEL File (.dat) |
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Bitmaps and JPEG files (.bmp, .jpg) |
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Molecular Modeling for Educators supports a number of connection table and graphics formats. This page describes this capability. Output and input of these files is through the "File" menu's "Open" and "Save" features. A file containing information on atom types, X, Y, Z coordinates and bond information is called a connection table. All of the connection tables (MDL Molfiles, MACROMODEL, Brookhaven protein database and CML) are standard formats using the ASCII character set. They are used by many other chemistry programs and can be used as a way of communicating between MMEd and other chemical programs. The clipboard copy and paste features can be used to create structures to paste into internet applications.
MDL Molfiles (.mol). MMEd supports input and output of this file format both from files (File menu) and over the text portion of the clipboard (Edit menu/ Copy or paste). It supports both the old format used by the old desktop MDL programs of the early 1990s and the newer space delimited format. Multiple molecules in a file and storage of formal charges is supported. This format is currently the most widely supported connection table format in chemistry.
CML is an attempt to improve on this format, particularly for internet applications.MACROMODEL files (.dat). MMEd supports an older version of this format from about 1995. It will both input and output files from disk. This format was developed at Columbia University in conjunction with their molecular modeling program MACROMODEL.
Brookhaven protein database files (.pdb, .ent). Input of these files is fully supported up to the 20,000 atom limit of MMEd. Output is limited, as MMEd does not output the amino acid residues and the comments, only atoms via the HETATOM keyword. The Brookhaven format is much more complex than other formats and contains a number of alternative ways of handling molecular geometry. It is typically used to store crystal structures of proteins and nucleic acid sequences.
SMILES notation. MMEd does not input SMILES notation, but it does output it from the Calculate menu. The output appears in a text box which can be edited. You can copy the SMILES notation to the clipboard by hitting the Copy button in the SMILES editor. The option of saving the SMILES to a file is also included in this procedure. SMILES was developed by Corwin Hansch and Albert Leo's QSAR research group at Pomona college and was used as input by them in their cLogP program.
Chemical Markup Language and XML: MMEd supports input and output of this file format both from disk (File menu) and over the clipboard (Edit menu/Copy or paste). The following built in functions are supported: Atom (id, element type, x, y and z (saved as both 2-D and 3-D), and formal charge. Bond: (atom 1, atom 2 and the bond type). CML is a modified version of XML and may be the standard connection table format in the future. MMP uses version 1.01.
http://www.xml-cml.org contains more information on this format. Efforts are underway to may this the standard chemical format for internet applications.MOPAC Input and Output files: MMEd opens and save MOPAC version 6 input and output files. It gives the input file the name for005. And the output file is called for005.mno. Note that these file names are specified by opening the Links editor from the File menu ("Initialize Links") and can be changed to connect to some other version of MOPAC other than the one provided.
Bitmaps and JPEG Files: MMEd will open Windows Bitmap files as a background drawing and will save the current screen image to either a bitmap or JPEG file from the File menu's Open and Save items. A more sophisticated JPEG editor and
HTML file creator is described on another web page. The program also support copying and pasting of the drawing window's image over the Window's clipboard (Edit menu - Copy and Paste). Of course, bitmaps and JPEG files store images, not chemical information - this will be lost when saving molecules in these formats.Clipboard input and output: From the Edit menu's Copy and Paste items you can send MDL Files, CML Files and graphics images to other applications. For Graphics images we find it is often best to edit the image either with the Image Processor found on the Tools menu or with a drawing program (Microsoft Paint works fine) before sending the image to a Word Processor or Presentation Graphics package as they usually need to be cropped.