Custom building Coot from source code

These instructions are current as of coot release 0.5.

The following is specific to Ubuntu linux, but should be generalizable to any recent linux distribution.

This is a so-called "advanced" task. Don't attempt it unless you would rather compile your own software than use pre-compiled versions. The standard (supported) method for installing Coot is to download a pre-compiled binary, or to use the autobuild scripts: Coot.

Install gpp4 and other dependencies on Linux.

Instead of using ccp4-onlylibs-dev, we want to use ssm, mmdb, gpp4 and clipper packages.

To keep things tidy, I suggest installing everything into /usr/local/xtal

Install these in the order described:

mmdb

wget http://www.ebi.ac.uk/~keb/cldoc/downloads/mmdb-1.19.tar.gz
./configure --prefix=/usr/local/xtal --includedir=/usr/local/xtal/include
make
make install

ssm

wget ftp://ftp.bioxray.au.dk/pub/mok/src/ssm-0.1.tar.gz
CPPFLAGS=-I/usr/local/xtal/include ./configure --prefix=/usr/local/xtal --includedir=/usr/local/xtal/include
make
make install

gpp4

wget ftp://ftp.bioxray.au.dk/pub/mok/src/gpp4-1.0.4.tar.gz
CPPFLAGS=-I/usr/local/xtal/include ./configure --prefix=/usr/local/xtal --includedir=/usr/local/xtal/include
make
make install

fftw

We need to compile fftw in a way that differs from that used to make the standard linux distribution of fftw. So to do that, we will install our own in /usr/local/xtal/lib, so it will remain hidden from the rest of the system, unless directed to look for it there.

ftp://ftp.fftw.org/pub/fftw/old/fftw-2.1.5.tar.gz
CPPFLAGS=-I/usr/local/xtal/include ./configure --prefix=/usr/local/xtal --includedir=/usr/local/xtal/include --enable-float
make
make install

clipper

wget http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper20ac.latest.tar.gz
CPPFLAGS=-I/usr/local/xtal/include ./configure --prefix=/usr/local/xtal --includedir=/usr/local/xtal/include -enable-shared --with-gpp4=/usr/local/xtal --with-mmdb=/usr/local/xtal --with-fftw=/usr/local/xtal --enable-mmdb --enable-minimol --enable-cif --enable-cns --enable-gpp4
make
make install

Note that if the primary server for the source code is down, you can often find what you need mirrored elsewhere, eg:

http://distfiles.msn.wi.us.finkmirrors.net/mirrors/fink/distfiles

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:

guile-lib (I had to compile this myself as described below)

goosh (I had to compile this myself)

guile-gui (I had to compile this myself)

guile-gtk-2.0 (I had to compile this myself)

net-htttp (I had to compile this myself)

To compile these, use the commands

configure --prefix=/usr
make
sudo make install

This puts stuff into /usr, rather than /usr/local or /usr/local/xtal, which you might not want to do. The aim is to eventually get these into the standard system distribution, in which case they will reside in /usr with the other guile extensions. All of these should work with guile-1.8.

Configuring and building coot

Start a root shell session

If root is enabled, log into a root shell, or else if you have sudo (debian, ubuntu, etc), use the command

sudo zsh 

(or whatever shell) to open a root shell, and issue the following commands as indicated.

Fix a configure bug

First, issue the following command to fix a configure bug when compiling with gpp4:

perl -pi -e 's|lccp4c|lgpp4|g' configure 

Now configure this way:

PATH="/usr/local/xtal/bin:$PATH" \
CPPFLAGS="-I/usr/local/xtal/include -I/usr/local/xtal/include/clipper -I/usr/local/xtal/include/gpp4 -I/usr/local/xtal/include/mmdb -I/usr/local/xtal/include/ssm" \
./configure --prefix=$PWD \
--with-gpp4=/usr/local/xtal \
--with-mmdb-prefix=/usr/local/xtal \
--with-ssmlib-prefix=/usr/local/xtal \
--with-clipper-prefix=/usr/local/xtal \
--with-fftw=/usr/local/xtal \
--with-glut-prefix=/usr --with-gl-prefix=/usr/X11R6 \
--with-gtk2 --with-gnomecanvas-prefix=/usr \
--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

Then, 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 coot:

make 
make -i install

To make it play nice with python, I have had to do the following:

perl pi -e 's|PYTHONHOME=\$COOT_PREFIX|\#PYTHONHOME=\$COOT_PREFIX|g' bin/coot
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-0.5 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-0.5/lib/data
cp -r dic /usr/local/xtal/coot-0.5/lib/data/monomers

Export the COOT_REFMAC_LIB_DIR variable

(you can edit bin/coot):

 export COOT_REFMAC_LIB_DIR=$COOT_PREFIX/lib

Notes on the above:

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).

 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

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).