New PPC version of 'FoldIt'‹ a protein modelling freeware

J.C. JESIOR jean-claude.jesior at imag.fr
Tue Jan 2 08:39:10 EST 1996


    ANNOUNCING THE NEW PPC VERSION OF 'FOLDIT (LIGHT)' v.4.1.1
    a molecular modelling freeware for Macintosh computers.
   €€€€€€€€€€€€€€€€€€€€€   FREEWARE   €€€€€€€€€€€€€€€€€€€€€

           €€€€ First release of the PPC version €€€€


DOWNLOAD

* Using a WWW browser 'FoldIt (light)' can be downloaded from the
following address:
              ftp://ftp.imag.fr/pub/TIMC/FoldIt.html
* Using 'Fetch', it can be downloaded directly from:
              ftp.imag.fr   in the directory:        pub/TIMC

***********************************************************************
You'll find two versions of the application:
* Download the 'FoldIt (light) FAT' version if you are using a Power Mac
or a Macintosh equipped with a 68LC040 CPU.
* Download the 'FoldIt (light) FPU' version if you are using a machine
equipped with a 68030 CPU (+68881/82 coprocessor) or with a full 68040 CPU
(not a 68LC040!)
***********************************************************************


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.
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 Macintosh computers running under system
7.0 and higher.
It has been developed with Symantec Think Pascal and includes 52000 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) FAT' runs on any Macintosh computers.
For those who are using Macintosh computers equipped with 68030 (+
coprocessor) or 68040 microprocessors (i.e. Macintosh SE30 to Quadras), a
version requirring FPU is also included in the package ('FoldIt (light)
FPU').
The application itself requires 879 KB - 1.9 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

A manual is included as a stand alone document which can be printed.
Several small size protein structures are included as example.
Balloon help is supported.

******************************************************
FoldIt (light)
freeware
by
Jean-Claude JÉSIOR/ CNRS, Grenoble, France
e-mail: jean-claude.jesior at imag.fr
Version 4.1.1 - Sunday, 24 December 1995
developed with Symantec Think Pascal.
FAT version compiled with Metrowerks Code Warrior.
******************************************************

-- 
Jean-Claude JESIOR
jean-claude.jesior at imag.fr




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