An Interactive Molecular Modeling Software
with Integrated Ruby Interpreter
- Version 0.5.0 build 20100121
+ Version 0.5.6.2 build 20110823
Toshi Nagata
Molby is a copyrighted product of Toshi Nagata.
- Copyright (C) 2009 Toshi Nagata
+ Copyright (C) 2009-2010 Toshi Nagata
Molby includes (more technically: is statically linked to) the following softwares, which are copyrighted products as described below:
- wxWidgets 2.8.9: Copyright (C) 1992-2008 Julian Smart, Robert Roebling, Vadim Zeitlin and other members of the wxWidgets team. Portions (c) 1996 Artificial Intelligence Applications Institute
- Ruby 1.8.7: Copyright (C) 1993-2009 Yukihiro Matsumoto
- CLAPACK: Copyright (c) 1992-2008 The University of Tennessee.
+- AmberTools 1.3: Copyright (c) Junmei Wang, Ross C. Walker, Michael F. Crowley, Scott Brozell and David A. Case
Molby is distributed under the GNU General Public License (version 2). See the file COPYING for more details.
(1) Mac OS X
-(i) Xcode
+(i) Xcode, gfortran
Install Xcode, if you have not done so yet. The Xcode project included in the source distribution is for Xcode 3.0 and later, thus you need Mac OS 10.5. It may work with Xcode 2.5 on Mac OS 10.4, but this have not been tested.
+To build AmberTools, you need to have gfortran installed. The author uses a binary build available at the "R for Mac OS X" website (http://r.research.att.com/tools/, gfortran-4.2.3.dmg).
+
+We need static linking of libgfortran.a. For that purpose, the following modification should be done after installation of gfortran.
+
+% cd /usr/local/lib
+% sudo cp libgfortran.a libgfortran-static.a # Copy as a different name
+% sudo strip -S libgfortran-static.a # Remove the symbols
+% sudo ranlib libgfortran-static.a
+
+The last two lines are necessary to avoid linker warnings saying "Can't find atom for N_GSYM stabs."
+
(ii) wxWidgets
Get wxMac-2.8.9.tar.gz from the wxWidgets page in sourceforge.net (http://sourceforge.net/projects/wxwindows/files/). Newer versions may work, but they are not tested.
The Windows binary is built by using MinGW/MSYS. If you use VC++ or Cygwin, you need to help yourself. I use Windows only occasionally, so there may be errors and misunderstandings in the following descriptions. Feedback is welcome!
-(i) MinGW and MSYS
+(i) MinGW, MSYS, gfortran
+
+Install MinGW and MSYS. The author uses MinGW-5.1.4 and MSYS-1.0.11.
-Install MinGW and MSYS. The default configuration should be sufficient.
+To build AmberTools, you need to have gfortran installed. The author has experienced problems with the gfortran of MinGW, and instead is using the binary build taken from http://quatramaran.ens.fr/~coudert/gfortran/ (version 4.5.0, 20090421, trunk revision 146519).
(ii) wxWidgets
$ cd $HOME/wxMSW-2.8.9
$ mkdir msw-build
$ cd msw-build
-$ ../configure --with-msw --with-opengl --disable-shared --enable-unicode --with-libjpeg-builtin --with-zlib=builtin
+$ ../configure --with-msw --with-opengl --disable-shared --enable-unicode --with-libjpeg=builtin --with-zlib=builtin
$ make
(You do not need to do "sudo make install".)
2010.1.21.
+2010.1.31. Added notice on AmberTools1.3
+2010.4.29. Update description for MinGW/MSYS
+2011.8.3. Added notice on static linking of libgfortran for Mac
+
Toshi Nagata