Coot: Difference between revisions

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==Installing Coot on Linux==
==Installing Coot on Linux==


Installing coot on linux is rather more straightforward than on OS X, because most linux systems are based on gnome and/or kde, and tend to have many of the required components already installed. Most of the other dependencies are also readily available (at least in Debian, so I assume this is the case for other package management systems as well).
Installing coot on linux is rather more straightforward than on OS X, because most linux systems are based on gnome and/or kde, and tend to have many of the required components already installed. Most of the other dependencies are also readily available.


===First, [[Install CCP4 on Linux]].===
=== Installation from a binary package ===
This is the recommended way for those who do not want to delve into the mysteries of compiling and linking a great but complex piece of software. Read the (somewhat outdated, it seems) [http://www.ysbl.york.ac.uk/%7Eemsley/coot/coot-faq.html Coot FAQ] to find "Additional Notes" for your operating system.
In short, just go to http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/  and pick a suitable binary, e.g.
coot-0.5-pre-1-revision-1003-binary-Linux-i386-fedora-5.tar.gz for a Red Hat Enterprise Linux 5 or CentOS-5 system (Fedora 6 corresponds to RHEL5, thus Fedora 5 binaries are OK).
 
Then un-tar it under /usr/local/src, and establish a symlink (ln -s) between /usr/local/bin/coot and the bin/coot of the freshly unpacked distribution.
 
If you then run coot, and the loader complains that a certain library is missing, just ask
yum whatprovides <thatlibrary>
and install the library, again using yum (assuming yum is available in your distribution, otherwise use apt or whatever is there for this purpose).
 
 
=== Installation from source code ===
 
====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.,
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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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.
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===
====Second, install a newer version of Clipper====
Get the latest clipper from
Get the latest clipper from


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  --enable-mmdbold --enable-cif --enable-minimol
  --enable-mmdbold --enable-cif --enable-minimol


===Third, make sure the other needed dependencies are installed===
====Third, make sure the other needed dependencies are installed====


These include at least the following dependencies:
These include at least the following dependencies:


====Ubuntu packages====
=====Ubuntu packages=====


A [[list of coot dependencies]] that is probably only a subset
A [[list of coot dependencies]] that is probably only a subset


====Others that you have to make yourself: ====
=====Others that you have to make yourself: =====


[http://arglist.com/guile/goosh-1.3/ goosh] (I had to compile this myself)
[http://arglist.com/guile/goosh-1.3/ goosh] (I had to compile this myself)
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===Fourth, configure and build coot like this:===
====Fourth, configure and build coot like this:====


Use sudo zsh (or whatever shell) to open a root shell, and issue the commands
Use sudo zsh (or whatever shell) to open a root shell, and issue the commands
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===If you want to make it portable===
====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 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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