FoldIt.ReadMe FoldIt (light) Version 4. 3.0 self-extracting binhexed archive code optimized for PowerPC processors *********************************************************************** The application has been compressed with StuffIt 1.5.1, then encoded with BinHex 4.0. After you've downloaded the file, use StuffIt Expander to auto-unpack it automatically. *********************************************************************** *********************************************************************** The file 'FoldIt_light_430.Hqx' contains the application and some examples (1.7 MB). The file 'FoldIt_light_Files.Hqx' contains a set of 20 PDB structure files (2.6 MB). *********************************************************************** This application works on MacOS compatible computers running under System 7 and higher. It can only runs on computers equipped with a PowerPC microprocessor. A 256-color monitor is recommended. Put the 'FoldIt Prefs' folder (delivered with this application) into the 'System Folder' (not in the Preference folder!). To make the best use of 'FoldIt (light)', you'll find three sources of help: 1/ The familiar Balloon help. 2/ An on-line Help. 3/ A printable stand alone document, 'FoldIt User Manual'. Three 'FoldIt (light)' binary files (suffix '.FIT') can be found in the 'FoldIt (light)' Folder. To start and get used to the program just double-click on the myoglobin file '1MBA.FIT'. Two other binary files ('Batch83.RamW' & 'Thr.trAng.StatW') shows the capabilities of 'FoldIt (light)' to batch process structural data. A PDB text file ('pdb3pcy.ent') has also been added to this folder as a remainder of what PDB files look like (in order to view this text file in a clean fashion, set font type to monaco 9). Finally, the text file 'HEM.PDB' containing the coordinates of an hem group illustrates the capability of 'FoldIt (light)' to display the structure of any compound as long as the PDB format is respected. WHAT 'FOLDIT (LIGHT)' DOES? 'FoldIt (light)' is a molecular modelling program to visualize and manipulate proteins. 'FoldIt (light)' is an interactive program with a user friendly interface. The goal of this program was to build an integrated environment in which statistical analysis as well 3D observations could be realized on PDB files without having to transfer files or swap machines. Our major underlying research project is still to try to improve the folding prediction methods (hence the name 'FoldIt'). This is also the sole desactivated feature in this released version (hence the adjective '(light)'). 'FoldIt (light)' is intented to provide the possibility to analyze proteins up to 1600 residues in size, to visualize and manipulate them interactively. It can directly read any protein coordinate text file from the Brookhaven Protein Data Bank (PDB) (Bernstein et al., 1977) including hetero-atoms and water molecules. 'FoldIt (light)' has two main windows: a color image window to display the protein structure and a text window to record the result of all operations requested by the user. The protein structure can be manipulated easily in real time with the mouse, zoomed or observed in stereo. Structure movement can also occur stepwise for a more precise control. Animations can be created. Steric conflicts, disulfide bonds, hydrogen and ionic interactions can be located and displayed in the protein structure. These interactions are also reported in the text window. Atoms and residues can be tagged individually (or globally) and structural information can then be extracted. Portions of a structure can be read into memory or displayed. Two structures can be read at the same time in memory and can be overlapped automatically. The second structure can be manipulated independently of the first. Bonds can be rotated and atomic parameters can be changed. The sequential folding of a protein can be simulated. It is possible to create a protein de novo from the menu or by entering the sequence from the keyboard. Structures can then be manipulated locally or forced into helices. Site directed mutations can be simulated. The application can process structures in the batch mode to extract a number of structural features: Ramachandran plots, SS-bond plots, H-bond plots. Statistics on atomic parameters are displayed as histograms. The content of image and text windows as well as histograms can be saved to disk. SOFTWARE ENVIRONMENT 'FoldIt (light)' can only work on MacOS compatible computers running under system 7.0 and higher. It has been developed with Symantec Think Pascal and includes 55000 lines of code. The application can run in the background which is convenient for lengthy statistical procedures. 'FoldIt (light)' does not support printing but can save the content of its text window (report of different operations and data analysis) and the content of the image window (result of graphic operations) in TEXT or PICT formats. These files can then be manipulated by other specialized applications and printed. HARDWARE ENVIRONMENT 'FoldIt (light)' runs on computers equipped with a PowerPC microprocessor The application itself requires 1.2 MB of memory and 3.3 KB of additional memory for each read residue: this means that 660 KB of extra RAM are necessary to read a typical 200-residue protein. Color monitors are preferred to give a better depth perception but black & white monitors may also be used. DOCUMENTATION On-line help as well as balloon help are supported. A printable stand alone document is provided. Several small size protein structures are included as example. ****************************************************** FoldIt (light) freeware by Jean-Claude JESIOR / CNRS, Grenoble, France e-mail: jean-claude.jesior@imag.fr Version 4.3.0 - 11 november 1997 developed in Pascal with Symantec Think & Metrowerks Code Warrior. ******************************************************