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There are also instructions for [[Custom building Coot from source code]]. This should not be attempted except by experts.
There are also instructions for [[Custom building Coot from source code]]. This should not be attempted except by experts.
====First, [[Install CCP4 on Linux]].====
I let ccp4 build its own fftw. Be sure to build the clipper libraries.  After you complete the default installation, go back to $CLIB/clipper/clipper/mmdbold and build some more libraries, i.e.,
cd  $CLIB/clipper/clipper/mmdbold
make
make install
to get the additional mmdbold libraries installed in their canonical location.  This should take care of the ccp4-type dependencies, as well as ensuring that you have fftw libs that play well with the clipper libraries.
====Second, install a newer version of Clipper====
Get the latest clipper from
wget http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.latest.tar.gz
I installed the latest clipper into /usr/local/xtal  It was a PITA to compile:
CPPFLAGS="-I$CLIB/src/mmdb" ./configure --prefix=/usr/local/xtal --with-fftw=$CCP4 \
--with-ccp4=$CCP4 --with-mmdb=$CLIB --enable-cns --enable-ccp4 --enable-mmdb \
--enable-mmdbold --enable-cif --enable-minimol
====Third, make sure the other needed dependencies are installed====
These include at least the following dependencies:
=====Ubuntu packages=====
A [[list of coot dependencies]] that is probably only a subset
=====Others that you have to make yourself: =====
[http://arglist.com/guile/goosh-1.3/ goosh] (I had to compile this myself)
[http://www.ossau.uklinux.net/guile/ guile-gui]  (I had to compile this myself)
[http://www.gnu.org/software/guile-gtk/ guile-gtk-2.0] (I had to compile this myself)
[http://www.ysbl.york.ac.uk/~emsley/software/extras/net-http-0.3.1.tar.gz net-htttp] (I had to compile this myself)
To do so, I used
configure --prefix=/usr
make
sudo make install
====Fourth, configure and build coot like this:====
Use sudo zsh (or whatever shell) to open a root shell, and issue the commands
CPPFLAGS="-I$CLIB/src -I$CLIB/src/mmdb" ./configure --with-mmdb-prefix=$CCP4 --with-clipper-prefix=/usr/local/xtal \
--with-fftw=$CCP4 --with-glut-prefix=/usr --with-gl-prefix=/usr/X11R6 --with-gtk2 --with-gnomecanvas-prefix=/usr \
--with-ssmlib-prefix=$CCP4 --with-imlib-prefix=/usr --with-gtkgl-prefix=/usr --with-glib-prefix=/usr --with-guile-gtk \
--with-guile-gtk-prefix=/usr  --with-gsl-prefix=/usr --with-guile --with-python --prefix=$PWD
Remake the  src/coot_wrap_python.cc and src/coot_wrap_guile.cc files
/bin/rm -f **/coot_wrap_**.cc
cd src
touch c-interface-database.hh
make coot_wrap_guile.cc
make coot_wrap_python.cc
cp coot_wrap_guile_pre.cc coot_wrap_guile.cc
cd ..
Now compile it:
make
make -i install
cp src/coot.py python/.
cp src/coot.py share/coot/python/.
Now add the reference structures:
cd share/coot
wget http://www.ysbl.york.ac.uk/~emsley/software/coot-reference-structures.tar.gz
tar xvfz coot-reference-structures.tar.gz ; rm coot-reference-structures.tar.gz
Now add the refmac dictionaries (eg using coot-0.4.1 and refmac 5.4; change as required):
cd /tmp
wget  wget http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
tar xvfz refmac5.4_dictionary.tar.gz
mkdir -p  /usr/local/xtal/coot-0.4.1/lib/data
cp -r dic /usr/local/xtal/coot-0.4.1/lib/data/monomers
Export the COOT_REFMAC_LIB_DIR variable (you can edit bin/coot):
  export COOT_REFMAC_LIB_DIR=$COOT_PREFIX/lib
The configure command is all one line; I've escaped the return. Using --prefix=$PWD simply keeps everything self-contained.  You can use any install prefix you want to (it defaults to /usr/local; another sensible choice is /usr/local/xtal.  Avoid /usr as a prefix, as it can mess with your system).
The make -i install is needed if you choose --prefix=$PWD because it tries to install some files where they are presently situated.
----
====If you want to make it portable====
You don't need to do this to run coot; this is only handy if you need to redistribute it (or make say a debian package).
You can see what dynamic libraries coot needs to load by issuing the command
ldd coot-real
or, if you just want to see the full path to the libraries, issue
ldd coot-real | awk '{print $3}' | grep -v fff | sort -u
You can use additional grep filters to select the ccp4 libs, clipper libs, eliminate coot's own libaries (that are already in the lib directory) and so forth.
(The '''ldd''' command is equivalent to '''otool -L''' on Mac OS X.)  Then you can copy these into coot's lib directory. I used the following commands in zsh to copy in the needed directories (this is overkill, but wtf).
<pre>
cd /usr/local/xtal/coot-0.1.2/bin
foreach dylib in $(ldd coot-real | awk '{print $3}' | grep -v fff | grep -v "usr/local/xtal/coot" | sort -u )
      print copying $dylib
      sudo cp -i $dylib /usr/local/xtal/coot-0.1.2/lib/.
end
</pre>
In addition, the guile modules can all be put in one centralized location:
cp -R /usr/share/guile* /usr/local/xtal/coot-0.1.2/share/.
Finally, you can give coot its own copy of the refmac monomers library:
mkdir -p /usr/local/xtal/coot-0.1.2/share/coot/lib/data
cp -R /usr/local/xtal/ccp4-6.0/lib/data/monomers /usr/local/xtal/coot-0.1.0-pre-3/share/coot/lib/data/.
Then edit /usr/local/xtal/coot-0.1.2/bin/coot and un-comment the appropriate environment variable lines (there are 2).


=Running Coot=
=Running Coot=
Kevin Cowtan
16

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