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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. |
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| ====First, [[Install CCP4 on Linux]].====
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| 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.,
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| cd $CLIB/clipper/clipper/mmdbold
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| make
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| make install
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| to get the additional mmdbold libraries installed in their canonical location. This should take care of the ccp4-type dependencies, as well as ensuring that you have fftw libs that play well with the clipper libraries.
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| ====Second, install a newer version of Clipper====
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| Get the latest clipper from
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| wget http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.latest.tar.gz
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| I installed the latest clipper into /usr/local/xtal It was a PITA to compile:
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| CPPFLAGS="-I$CLIB/src/mmdb" ./configure --prefix=/usr/local/xtal --with-fftw=$CCP4 \
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| --with-ccp4=$CCP4 --with-mmdb=$CLIB --enable-cns --enable-ccp4 --enable-mmdb \
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| --enable-mmdbold --enable-cif --enable-minimol
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| ====Third, make sure the other needed dependencies are installed====
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| These include at least the following dependencies:
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| =====Ubuntu packages=====
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| A [[list of coot dependencies]] that is probably only a subset
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| =====Others that you have to make yourself: =====
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| [http://arglist.com/guile/goosh-1.3/ goosh] (I had to compile this myself)
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| [http://www.ossau.uklinux.net/guile/ guile-gui] (I had to compile this myself)
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| [http://www.gnu.org/software/guile-gtk/ guile-gtk-2.0] (I had to compile this myself)
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| [http://www.ysbl.york.ac.uk/~emsley/software/extras/net-http-0.3.1.tar.gz net-htttp] (I had to compile this myself)
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| To do so, I used
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| configure --prefix=/usr
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| make
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| sudo make install
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|
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| ====Fourth, configure and build coot like this:====
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| Use sudo zsh (or whatever shell) to open a root shell, and issue the commands
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| CPPFLAGS="-I$CLIB/src -I$CLIB/src/mmdb" ./configure --with-mmdb-prefix=$CCP4 --with-clipper-prefix=/usr/local/xtal \
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| --with-fftw=$CCP4 --with-glut-prefix=/usr --with-gl-prefix=/usr/X11R6 --with-gtk2 --with-gnomecanvas-prefix=/usr \
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| --with-ssmlib-prefix=$CCP4 --with-imlib-prefix=/usr --with-gtkgl-prefix=/usr --with-glib-prefix=/usr --with-guile-gtk \
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| --with-guile-gtk-prefix=/usr --with-gsl-prefix=/usr --with-guile --with-python --prefix=$PWD
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| Remake the src/coot_wrap_python.cc and src/coot_wrap_guile.cc files
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| /bin/rm -f **/coot_wrap_**.cc
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| cd src
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| touch c-interface-database.hh
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| make coot_wrap_guile.cc
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| make coot_wrap_python.cc
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| cp coot_wrap_guile_pre.cc coot_wrap_guile.cc
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| cd ..
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| Now compile it:
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| make
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| make -i install
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| cp src/coot.py python/.
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| cp src/coot.py share/coot/python/.
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| Now add the reference structures:
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| cd share/coot
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| wget http://www.ysbl.york.ac.uk/~emsley/software/coot-reference-structures.tar.gz
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| tar xvfz coot-reference-structures.tar.gz ; rm coot-reference-structures.tar.gz
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| Now add the refmac dictionaries (eg using coot-0.4.1 and refmac 5.4; change as required):
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| cd /tmp
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| wget wget http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
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| tar xvfz refmac5.4_dictionary.tar.gz
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| mkdir -p /usr/local/xtal/coot-0.4.1/lib/data
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| cp -r dic /usr/local/xtal/coot-0.4.1/lib/data/monomers
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| Export the COOT_REFMAC_LIB_DIR variable (you can edit bin/coot):
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| export COOT_REFMAC_LIB_DIR=$COOT_PREFIX/lib
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| The configure command is all one line; I've escaped the return. Using --prefix=$PWD simply keeps everything self-contained. You can use any install prefix you want to (it defaults to /usr/local; another sensible choice is /usr/local/xtal. Avoid /usr as a prefix, as it can mess with your system).
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| The make -i install is needed if you choose --prefix=$PWD because it tries to install some files where they are presently situated.
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| ----
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| ====If you want to make it portable====
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| 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).
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| You can see what dynamic libraries coot needs to load by issuing the command
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| ldd coot-real
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| or, if you just want to see the full path to the libraries, issue
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| ldd coot-real | awk '{print $3}' | grep -v fff | sort -u
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| 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.
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| (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).
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| <pre>
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| cd /usr/local/xtal/coot-0.1.2/bin
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| foreach dylib in $(ldd coot-real | awk '{print $3}' | grep -v fff | grep -v "usr/local/xtal/coot" | sort -u )
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| print copying $dylib
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| sudo cp -i $dylib /usr/local/xtal/coot-0.1.2/lib/.
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| end
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| </pre>
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| In addition, the guile modules can all be put in one centralized location:
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| cp -R /usr/share/guile* /usr/local/xtal/coot-0.1.2/share/.
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| Finally, you can give coot its own copy of the refmac monomers library:
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| mkdir -p /usr/local/xtal/coot-0.1.2/share/coot/lib/data
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| cp -R /usr/local/xtal/ccp4-6.0/lib/data/monomers /usr/local/xtal/coot-0.1.0-pre-3/share/coot/lib/data/.
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| Then edit /usr/local/xtal/coot-0.1.2/bin/coot and un-comment the appropriate environment variable lines (there are 2).
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| =Running Coot= | | =Running Coot= |