-
Notifications
You must be signed in to change notification settings - Fork 0
Protein structure prediction program based on distance geometry.
License
aaszodi/dragon
Folders and files
Name | Name | Last commit message | Last commit date | |
---|---|---|---|---|
Repository files navigation
README.txt ========== The SGI distributions --------------------- The DRAGON package for SGI comes in three flavors, i.e. the executables are compiled for the three SGI application binary interfaces (ABIs). The gzip-compressed tarfiles are called dragon-<VERSION>-<ABI>.tar.gz where <VERSION> is the version number like "4.18.0", and <ABI> is "irix-o32","irix-n32" or "irix-n64". Choosing the right SGI Application Binary Interface (ABI) --------------------------------------------------------- The 'irix-o32' executables can be run on any SGI R4k/R5k/R8k/R10k system under IRIX 5.3 and above that supports the MIPS-II instruction set. Use this ABI if you have not upgraded from IRIX 5.3 yet for some reason. Note that o32 will not be supported in the future. The 'irix-n32' executables can be run on any SGI R4k/R5k/R8k/R10k system under IRIX 6.2 that supports the MIPS-III instruction set. I recommend that you use this ABI. The 'irix-n64' executables can be run on SGI R8k/R10k systems under IRIX 6.2 and above, using the MIPS-IV instruction set: the only exceptions are O2 machines running IRIX 6.3 which do NOT support the 64-bit ABI even with an R10000 processor. The 'n64' executables were optimised for the R10000 processor but they run on R8000-based machines as well. There is no support for the Intel-based SGI workstations running Windows NT. The IBM PC distribution ----------------------- This is contained in the compressed tarfile dragon-<VERSION>-linux.tar.gz. DRAGON can be run on IBM PCs and compatibles having Intel 486, Pentium and Pentium II processors or compatibles under Linux 2.0.x in ELF executable format. If you have XFree86 installed and your X server is capable of displaying 16-bit colours, then you can even enjoy the OpenGL graphics output, thanks to Brian Paul's MESA library. Some features do not work yet, due to bugs in GCC (version 2.8.1). There is no DOS or Windows version of DRAGON. The SUN distributions --------------------- Executables are provided in the compressed tarfiles dragon-<VERSION>-<ARCH>.tar.gz where <ARCH> is 'solaris-sparc' for SPARC processors or 'solaris-x86' for Intel-based systems. Unfortunately OpenGL graphics is not supported by these executables. Instructions for installing the DRAGON executables -------------------------------------------------- 1) Create a directory where you want DRAGON to live (say /usr/local/dragon4). 2) Copy the compressed tarfile to it. Uncompress and expand the distribution. The executables will be expanded into the 'bin/<ARCH>' directory where <ARCH>={irix-o32|irix-n32|irix-n64|linux|solaris-sparc|solaris-i86}. In addition, the following subdirectories will be created:- 'data': default data files 'doc': documentation 3) Edit the 'startup-<ARCH>.csh' file in the 'bin/startup' directory so that the variable DRAGON_ROOT is set to the DRAGON location (/usr/local/dragon4 in our example). You may have to edit the PVM_LOCATION variable to tell the program where to look for PVM (if installed). For the irix-n32 architecture, make sure that you have the n32 ABI version of the PVM libraries. Then source the file. It is recommended to source 'bin/startup/startup-<ARCH>.csh' from the .cshrc files of those users who access DRAGON regularly. Executables ----------- These can be found in the subdirectories of the 'bin' directory. 'dragon': the DRAGON program itself 'secmap': a program for mapping secondary structure assignments onto the target sequence in comparative modelling 'rank': a program that helps you to rank the models according to various scores 'sidech': a partial side-chain constructing program to be used in comparative modelling 'hbassign': a tool for generating hydrogen bond assignments to be used with QUANTA 'clumsy': a simple clustering program to generate families from structures produced by DRAGON PVM support ----------- DRAGON can run in parallel using the Parallel Virtual Machine (PVM). However, you have to obtain and install PVM yourself as it is not part of this distribution. Try anonymous FTP from NETLIB or a mirror site near to you. If you want to use PVM, then set the PVM_ROOT environment variable in 'startup-<ARCH>.csh' appropriately. Consult the PVM User Guide for details on how to set up PVM. Data files ---------- These live in the 'data' subdirectory. If you set up an environment variable "DRAGON_DATA" pointing to this directory then you can refer to these files in the DRAGON parameter file using the $DRAGON_DATA macro. Refer to the User Guide for details. Documentation ------------- The complete DRAGON User Guide is the HTML document 'ug.html' in the 'doc' subdirectory. Users are strongly encouraged to read it before attempting to use the programs. Some outdated manual pages can be found in the 'doc/man1' subdirectory which can be moved to more convenient locations. Manpages may be slightly out of sync with respect to the User Guide: when in doubt, rely on the User Guide. Bugs ---- Bug reports may be sent to me (aaszodi@nimr.mrc.ac.uk). Reply and bug fixes are not guaranteed. Support ------- There is essentially none as I have discontinued active development since I left the National Institute for Medical Research in 1996. Sporadic updates and bug fixes may happen from time to time, though. In general, I will not provide tutorials. Please note that my present employer, the Novartis Forschungsinstitut GmbH does not endorse this package in any way. Copyright information --------------------- Copyright (C) 1993-1997. Andras Aszodi, William R. Taylor. The DRAGON program suite is distributed free of charge. The copyright holders therefore undertake no warranty of any kind, as detailed the "NO WARRANTY" section below which was taken from the GNU General Public License:- -------------------- Copyright (C) 1989, 1991 Free Software Foundation, Inc. 675 Mass Ave, Cambridge, MA 02139, USA NO WARRANTY BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. --------------------
About
Protein structure prediction program based on distance geometry.
Resources
License
Stars
Watchers
Forks
Packages 0
No packages published