Executable files have abbreviations related to hardware and operating system:
Two files need to be downloaded:
creating a user environment.
In order to install MAIN, create a directory where MAIN shall reside:
> mkdir MAIN > cd MAIN
"Untar" the downloaded "main_distribution.tar.gz" and gunzip the executable files into that directory.
> tar -zxvf main_distribution.tar.gz > chmod 755 mainps*.gz
Addopt the "login_BASH" or "login_CSH" files using a text editor like Emacs.
for the first time users:
> cp login_BASH login_BASH_by_own > cp login_CSH login_CSH_my_own
edit the login files for BASH environment. These environments need to be properly assigned. (I use /usr/local/progs/ for scientific software depository.) Note that LINUX and OSX require different "login_BASH..." files.
MASTER_LOCAL=/usr/local/progs export MASTER_LOCAL
MAIN=$MASTER_LOCAL/MAIN/ export MAIN
PURY=$MASTER_LOCAL/PURY/ export PURY PURY_EXE=$PURY"pury/pury.exe_32" export PURY_EXE
CE_SUPERIMPOSE=$MASTER_LOCAL/CE_superimpose/jfatcat/ export CE_SUPERIMPOSE
Compiling from the source using appropriate makefile. Choose the appropriate one in the source directory.
alias lgf='make -f $MAIN"source/makefile.LINUX_G95-64"
> emacs login_CSH
setenv MAIN /disk/username/main/
then define appropriate aliases for the executables to be used:
alias mainps $MAIN"mainps_2019.exe_LINUX...."
for compilation from the source
alias l95 'make -f $MAIN"source/makefile.LINUX_GFORT-64"
Integrate the "login_BASH" or "login_CSH" files into your working environment. BASH and CSH users insert appropriate line
source /disk/username/main/login_BASH_my_own source /disk/username/main/login_CSH_my_own
into your local startup file. For personal installations this would be in ".bashrc" or ".cshrc" files, wheres for a larger user community the system manager will normally provide other solutions.
Reopen your command line terminal for the settings to take effect.
Now try to run to see if there are shared libraries missing from your installation.
On LINUX you need gfortran, X11, OpenGL libraries installed.
How to start a MAIN session is described in the MAIN_DOC:documentation.HTML
Configurations for specific platforms
Advices for LINUX
Use accelerated drivers. The graphics drivers that come with the system are unsuitable for work.
NVIDIA or ATI cards are in general OK. I used to preffer the ATI cards due to higher quality line antialiasing. However, recently ATI drivers cased too many installation problems in so that the ability to install a driver is now the major factor of choice - so I preffer NVIDIA.
Stereo works where ever it is supported.
If you have SG dials you can use them XFree 4.2 based X11 server.
If you have problems compiling the module get it from the anonymous server as well.
and copy it to the proper location:
chmod +x dialbox_drv.o cp dialbox_drv.o /usr/X11R6/lib/modules/input/dialbox_drv.o
Macs (Apple computers)
MAIN is compiled for INTEL processors in 64 bit architecture
Compiling from the source
For the following platforms makefiles are made available in the source directory.
make -f my_makefile
will create a "new.exe_LINUX_GFORT-64", which you can rename to your favorable pet name you use for main.
GFORTAN can be used to, it does create some instability of the executable, due to the different compilation of the "if" statements.
The Perl-Tk package (Tk-804.030.tar.gz or higher) needs to be installed in order to be able to configure your working environmnet using a Tk based GUI. (You can download from http://www.perl.com/). It works on MACs as well as on LINUX distributions. The 64bit architecture requires change of the library path "/usr/X11/lib" into "/usr/X11/lib64". The simplest way is to edit the "Makefile".
When not provided by your system, you can install it through CPAN.
perl -MCPAN -e shell ... (accept defaults) install Tk
or use "yum" or similar
yum install perl-Tk
On many system including MAC OS X Tk installation exists with an error. In such cases do not use CPAN to install the Tk library. Instead download the tgz file, compile it, disregard the test out come and install it.
perl Makefile.PL make make install
occasionally the "Perl:LWP" module is missing and can be installed via CPAN.
perl -MCPAN -e shell install LWP
These additional sofwtare needs to be in your PATH. (See also the main page "other used programs".)
The "FatCat" and "CE" need their own environment "CE_SUPERIMPOSE". This way it is set in the "login_BASH":
CE_SUPERIMPOSE=$MASTER_LOCAL/CE_superimpose/jfatcat/ export CE_SUPERIMPOSE
You can get "FatCat" and "CE" from http://source.rcsb.org/jfatcatserver/download.jsp"
In order to run them from MAIN "superimpose", the original macros "runFatcat.sh" and "runCE.sh" have to be modified accordingly:
JDIR=$CE_SUPERIMPOSE; cpath="$JDIR/core.jar:$JDIR/structure.jar:$JDIR/structure-gui.jar:$JDIR/alignment.jar:$JDIR/JmolApplet.jar:$JDIR/javaws.jar:$JDIR/biojava3-core.jar:$JDIR/biojava3-alignment.jar" java -Xmx500M -cp $cpath org.biojava.bio.structure.align.fatcat.FatCat $args
The graphic renderes you can find at: -<A HREF=http://skuld.bmsc.washington.edu/raster3d/ TARGET="_blank>Rendering with RASTER3D</A> -<A HREF=http://www.povray.org/ TARGET="_blank>Rendering with POV-Ray</A>
MAIN use dynamical memory allocation. Default MAIN has allocated memory for 100 000 atoms, whereas maps and structure factors are allocated on the fly.
The show size command gives you the sizes of data arrays:
MAIN> show size Atoms arrays size .... 100000 Residue arrays size .. 30000 Pairs array size .... 100000 H-bonds array size ... 10000 Points arrays size ... 1000000 Topology library residues ... 150 Topology library atoms ...... 4500 Paramter classes ..... 300 Paramter bonds ....... 600 Paramter angles ...... 1000 Paramter dihedrals.... 1400 Paramter impropers.... 1000 Number of maps ................... 10 Total grid point size of maps .... dynamical Structure factors arrays size .... 17009
From the listed only the number of maps is fixed to 10.
The array sizes can be modified also from the MAIN command line:
MAIN> set sizes ? CMD_WRITE_FILE> HELP: POSSIBLE CONTINUATIONS: default initiali atoms hbonds pairs points residues topology paramete help
You can start MAIN with the modified sizes of ATOM and RESIDUE arrays
$ mainps --help GET_COMMAND_LINE> possible MAIN command line arguments: --atoms nn --residues nn --nodisplay --nostartup --geometry x y width height --help
$ mainps --atoms 500000 residues 40000
Tailoring your own documentation scripts
Documentation is part of your local distribution. The file tree is in a main/doc/.
The MAIN documentation is stored in the main/doc directory. Original files are editable ASCII text files "*.txt" and "*.HTML" found in the doc directory. They are converted via "Makefile" scripts into LaTeX (*.tex) and HTML *.html" files. You may wish to modify these scripts as well as documentation files. The command
creates all missing ".tex" and ".html" files from their ".txt" and ".HTML" files,
> make latex
creates three dvi files via LaTeX (users_guide.dvi, dialog_manual.dvi, ref_manual.dvi) and converts them into corresponding PostScript files. The three major LaTeX files are users_guide.tex, dialog_manual.tex and ref_manual.tex. Their headers assign the main character and page sizes. If you have LaTeX installed on your system and you are not satisfied with the page size or anything else you may create the 'ps' files explicitly with other tools.
> make latex_US
is an adaptation of 'make latex' which creates 'ps' files in the US letter size on the basis of users_guide_US.tex, dialog_manual_US.tex and ref_manual_US.tex. The 'US.tex' files are created with a different head (latex_head_US.txt) in front of the LaTeX manual structure file (as is users_guide.txt). So all you have to do it to create your 'heads' and correspondingly modify the 'Makefile'.
> make clean
will delete every file that can be derived from the originals via the to_tex converters, LaTeX and dvips. (If you are using dvi2ps adapt the 'Makefile'.)