Coot: Difference between revisions

676 bytes removed ,  20 December 2017
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→‎building loops: Fix website references
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==== Example: installing a 64bit nightly CentOS5 binary build on 64bit SL6.1 ====
==== Example: installing a 64bit nightly CentOS5 binary build on 64bit SL6.1 ====
First of all, SL (Scientific Linux) is a derivative of RHEL, as is CentOS. So all three OSs behave exactly the same.
First of all, SL (Scientific Linux) is a derivative of RHEL, as is CentOS. So all three OSs behave exactly the same.
The binaries with "x86_64" binaries are for 64bit systems; the "i386" binaries are for 32bit systems. Since my notebook is 64bits ("uname -a" reports "x86_64" more than once), I download ftp://turn5.biologie.uni-konstanz.de/coot/software/binaries/nightlies/pre-release/coot-0.7-pre-1-revision-3999-binary-Linux-x86_64-centos-5-python-gtk2.tar.gz (the main server is slow, so I use the mirror). As root, I "cd /usr/local/src" and un-tar. Next, have to find out which libraries are missing. This can be achieved by (''note the use of LD_LIBRARY_PATH in the second command - do not permanently modify LD_LIBRARY_PATH !''):
The binaries with "x86_64" binaries are for 64bit systems; the "i386" binaries are for 32bit systems. Since my notebook is 64bits ("uname -a" reports "x86_64" more than once), I download coot-0.7-pre-1-revision-3999-binary-Linux-x86_64-centos-5-python-gtk2.tar.gz. As root, I "cd /usr/local/src" and un-tar. Next, have to find out which libraries are missing. This can be achieved by (''note the use of LD_LIBRARY_PATH in the second command - do not permanently modify LD_LIBRARY_PATH !''):
  [root@localhost]# cd coot-Linux-x86_64-centos-5-gtk2-python
  [root@localhost]# cd coot-Linux-x86_64-centos-5-gtk2-python
  [root@localhost]# LD_LIBRARY_PATH=lib ldd bin/coot-real | grep found  
  [root@localhost]# LD_LIBRARY_PATH=lib ldd bin/coot-real | grep found  
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and make it executable with  
and make it executable with  
  chmod a+x /usr/local/bin/coot
  chmod a+x /usr/local/bin/coot
=== Installation on Debian/Ubuntu from debian archive files ===
As an alternative, you might wish to exploit the debain dpkg/apt/synaptic package management system on Ubuntu and other Debian linux distributions using (unofficial)
[http://diablo.ucsc.edu/~wgscott/debian/coot_hardy/  pre-compiled debian packages for coot and its dependencies]. (These will be discontinued when official packages become available.)
To do so, simply download the deb files and install with the command
sudo dpkg -i *.deb
dpkg will complain if a dependency is missing rather than install a broken program.
=== Packages for Ubuntu ===
A pre-packaged version of Coot (0.7-pre-1) for Ubuntu is available from mok0's Personal Package Archive (PPA) on Launchpad. Currently, packages for Ubuntu 10.04 (Lucid) and 10.10 (Maverick) are available.
To install the coot package on your system, you first need to install the public key for mok0's PPA:
  sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 1DC81A57
Next, add the PPA repository to your /etc/apt/sources.list file:
  sudo add-apt-repository ppa:mok0/ppa
That's it! Now, you should be able to:
  apt-get update && apt-get install coot
This version of Coot only supports the Python scripting language.
=== Mandriva Installation ===
To install the coot on Mandriva 2010.0 use the ubuntu distribution:
tar zxf coot-0.6.2-binary-Linux-i686-ubuntu-8.04.1-python-gtk2.tar.gz
in the .cshrc file:
alias coot  'source /prog/CCP4/ccp4-6.1.13/include/ccp4.setup-csh ; /prog/coot-Linux-i686-ubuntu-8.04.1-gtk2-python/bin/coot'
=== Converting to rpm packages ===
You can convert any debian package file into an rpm file using the program ''alien''.  I have done this and have made the [http://diablo.ucsc.edu/~wgscott/debian/rpm/coot/ resulting packages] available.


=== Installation from source code via autobuild scripts ===
=== Installation from source code via autobuild scripts ===
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[[morph_residues_gui.py]]
[[morph_residues_gui.py]]
===Example 5: Ensemble GUI===
GUI to allow navigation through structural ensembles as obtained e.g. from ensemble refinement:
[[ensemble_plugin.py]]


==Python to Scheme and return==
==Python to Scheme and return==
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A: there are 2 loop fitting tools in Coot
A: there are 2 loop fitting tools in Coot


# C alpha -> Mainchain [http://lmb.bioch.ox.ac.uk/coot/doc/coot.html#C_002dalpha-_002d_003e-Mainchain],[http://lmb.bioch.ox.ac.uk/coot/doc/coot.html#Building-Links-and-Loops]
# C alpha -> Mainchain [http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#C_002dalpha-_002d_003e-Mainchain],[http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Building-Links-and-Loops]
# DB Loop: (No good documentation) [http://lmb.bioch.ox.ac.uk/coot/doc/coot/protein_002ddb_002dloops.html#protein_002ddb_002dloops] Extensions -> Modelling -> DB Loop...  
# DB Loop: (No good documentation) [http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#protein_002ddb_002dloops] Extensions -> Modelling -> DB Loop...


==LSQ superpositions==
==LSQ superpositions==
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A: It used to be 0.167, I think.
A: It used to be 0.167, I think.
== Molprobity not active in COOT ==
Q: I am using COOT 0.8.1 EL that comes with the CCP4 6.5.010 on my Mac OS X 10.10.2. I wanted to run molprobity but the Validate > Probe clashes button in my pull down menu is not active. Is this function available in this COOT version?
A: Reduce and probe are separate programs available from the Richardson’s lab at Duke http://kinemage.biochem.duke.edu/. Download and install on your box. Then coot needs to be told in some instances where it can find these executables. I have the following lines in my ~/.coot file in Linux.
<pre>
;; .coot
;; This file is required. As of coot 0.8pre no other mechanism for
;; enabling probe in coot works
;;
;; This is full pathname of molprobity's probe program
(define *probe-command* "/apps/xray/bin/probe")
;; This is full pathname of molprobity's reduce program
(define *reduce-command* "/apps/xray/bin/reduce")
</pre>
Untried: if you have Phenix installed: it comes with phenix.probe and phenix.reduce - you could insert the paths to these binaries into the above definitions.
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