sundinKC@dna.lth.se (Anders Sundin Oragnisk kemi 2) (09/17/90)
MacMimic is an application for the display, construction and comparison of molecular models in full 3-D. It runs on the Macintosh II family of computers with a 256 colour monitor and 2 MBytes of memory. A demo of MacMimic version 1.0 is available via anonymous ftp from pollux.lu.se as macmimic_demo.sit.hqx. The demo has all functionalities of MacMimic except: The demo can not save or print documents. Copy and Paste only works within the demo. MM2(87) is not included. MacMimic is distributed by: Instar Software AB Research Park IDEON S-22370 Lund, Sweden The Macintosh interface. The Macintosh interface is fully implemented. MacMimic can handle multiple windows, and runs both under the Finder and the Multifinder. Most tools of MacMimic are placed in palettes and are therefore convenient to use. The standard Apple, File and Edit menus are available. Undo works on every command that changes the structure of a model. Copy and Paste can be used to move models between display windows or to the Scrapbook. Making pictures. A picture of a model can be copied from a display window to be included in a word processing document. Printing in black and white or in colour is available directly from MacMimic. Colour printing can be performed on any colour printer with a Macintosh compatible printer-driver. The colours used in printing can be customized through the Preferences dialog. Displaying models. MacMimic can display and handle structures with up to 32000 atoms. A large number of molecules can be displayed simultaneously in each of the windows of MacMimic. Molecules are displayed as stick or ball-and-stick models, each with toggable attributes such as atom labels, atom index and stereo. Colour is used to indicate atom type, but individual atoms or whole structures can be painted in other colours. The 3-D impression of models is improved by a configurable depth cueing. Input of structures. In addition to documents created by MacMimic, structures can be input from the MolLib library of structures, or obtained from a database as a PDB file (Brookhaven Protein Database file) or as an XR file (Cambridge Crystallographic Database file). Structures can also be imported and exported to the Macintosh applications Ball&Stick and Chem3D. Construction of models. MacMimic has a powerful structure editor which can create new and modify existing models. Atom type, charge and hybridization can be set for any atom. The bond lengths and the number of ligands are automatically adjusted. A set of substituents is available from a palette to make instant substitutions of any monovalent atom. The new dihedral angles and bonds are adjusted to make a low energy conformer. Any two models can be joined (substituted) or fused to create spiro compounds or complex ring systems. Chiral control. Chiral control is automatically achieved as all models are displayed and handled in full 3-D. The Enantiomer menu command changes a selected model to its mirror image. The Swap Substituents tool can be used to let any two substituents of an atom switch places. This tool provides a convenient way to switch absolute configurations (R<=>S), equatorial and axial substituents, and cis and trans isomers (Z<=>E). Comparison of models. Pseudo-atoms can be placed at the geometrical center of a number of atoms, or at the extension of a bond. Models can be compared by superimposition. Up to eight models can be superimposed (RMS fitted) simultaneously. Energy minimization of molecules. The MacMimic package includes the molecular mechanics program MM2(87). The MM2(87) User's Manual provides a detailed and authorative description of MM2(87). All computational options (for instance dihedral drivers, restricted motion, etc.) of MM2(87) can be accessed through an interactive input interface. MM2(87) can be run as a background task. sundinKC@dna.lth.se ok2aps@seldc52.bitnet Anders Sundin
kristoff@genbank.bio.net (David Kristofferson) (09/18/90)
Your posting about MacMimic looks perilously like commercial advertising and is not a proper use of the networks unless I missed something in your message. Please refrain from such acts in the future unless you are prepared to disclaim any connection with Instar Software. -- Sincerely, Dave Kristofferson GenBank Manager kristoff@genbank.bio.net
Don.Gilbert@IUBio.Bio.Indiana.Edu (Don Gilbert) (09/19/90)
In article <1990Sep17.112800.2874@lth.se> sundinKC@dna.lth.se (Anders Sundin Oragnisk kemi 2) writes: > MacMimic is an application for the display, construction and comparison of > molecular models in full 3-D. It runs on the Macintosh II family of > computers with a 256 colour monitor and 2 MBytes of memory. > > A demo of MacMimic version 1.0 is available via anonymous ftp from > pollux.lu.se as macmimic_demo.sit.hqx. The demo has all functionalities This looks like a fairly nice program. I have just tried it with a tRNA molecule from the Brookhaven databank (around 1600 atoms) which it draws in less than 10 minutes on a slow Mac II. In contrast, the Chem 3D program can't draw an 800 atom structure in 2 hours (when I gave up). You can now also find a copy of the demo version of this program via anonymous ftp to iubio.bio.indiana.edu, cd [archive.chemistry.mac], get macmimic-demo.hqx. You can also find a demo copy of ball&stick there. I have no affiliation with Instar software, the developer of MacMimic. I do hope that Bionet will allow informational messages about commercial software, such as the original posting. Anders did not, in my opinion, cross the line from useful information into advertising. -- Don Don.Gilbert@iubio.bio.indiana.edu biology dept., indiana univ., bloomington, in 47405, usa
kristoff@genbank.bio.net (David Kristofferson) (09/20/90)
Don, It is perfectly legitimate for postings about commercial software to be made on BIO-SOFTWARE/bionet.software. The restriction is that they should not be made by people with a financial interest in the software. The usual procedure when discussing commercial software is to do as you did, i.e., end with a disclaimer that the poster has no commercial interest in the software. This, of course, works on the honor system, but if repeated abuse is discovered steps can be taken to terminate a site's network access. -- Sincerely, Dave Kristofferson GenBank Manager kristoff@genbank.bio.net