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Coot is a graphics program for building, refining and analysing macromolecular models obtained with crystallographic procedures.
Coot is a graphics program for building, refining and analysing macromolecular models obtained with crystallographic procedures.


There is a [http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/ homepage] with extensive [http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/ documentation]. The program may be downloaded for Linux and Windows computers from the [http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/binaries/pre-release/ primary server]. The license of Coot is GNU GPL.  
There is a [http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ homepage] with extensive [http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/ documentation]. The program may there be [http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/binaries/release downloaded] for Linux and Windows. There's also Paul Emsley's [https://pemsley.github.io/coot/ coot blog]. The license of Coot is GNU GPL.  


=Installing Coot=
=Installing Coot=
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==Installing Coot on Windows==
==Installing Coot on Windows==
Please refer to [https://github.com/bernhardcl/coot/releases Bernhard Lohkamp's WinCoot download] page.
Please refer to [http://bernhardcl.github.io/coot/ Bernhard Lohkamp's WinCoot download] page. Or check manually on
[https://github.com/bernhardcl/coot/releases GitHub].


==Installing Coot on Linux==
==Installing Coot on Linux==
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=== Installation from a distributed binary tarball package ===
=== Installation from a distributed binary tarball 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.
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 [https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ Coot documentation] to find out about the details.


In short, just go to https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/ and pick a suitable binary, e.g.
In short, just go to https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/ and pick a suitable binary, e.g.
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=== Installation from source code via autobuild scripts ===
=== Installation from source code via autobuild scripts ===


Installation of coot and all of its dependencies are handled automatically through the autobuild scripts. There are two versions:
Go to https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/build-install-coot-from-scratch.html
* [http://www.ysbl.york.ac.uk/~emsley/build-logs/build-it GTK1] - the old user interface. This script builds coot and all its dependencies.
* [http://www.ysbl.york.ac.uk/~emsley/build-logs/build-it-gtk2-simple GTK2] - the new user interface. This script builds coot and most of the dependencies, excluding GTK2.
 
To build Coot, all you should need to do is edit a few settings in the top of the build script, or alternatively specify those settings as environment variables. For example, the following sequence of instructions will build the latest pre-release of the GTK 2 version with python support:
 
wget http://www.ysbl.york.ac.uk/~emsley/build-logs/build-it-gtk2-simple
export AUTOBUILD_INSTALLED=${HOME}/autobuild/coot
export AUTOBUILD_BUILD=${HOME}/autobuild/
export LOGS=$AUTOBUILD_BUILD/logs
export NIGHTLY_DEST_DIR=$AUTOBUILD_BUILD
export STABLE_DEST_DIR=$AUTOBUILD_BUILD
export build_coot_prerelease=1
bash build-it-gtk2-simple python > build.log
(This script works in bash. For tcsh, replace 'export' with 'setenv' and '=' with ' '.
 
In some cases you may need to download additional development packages in order to build all the components.
 
=== Installation from source code manually ===
 
There are also instructions for [[Custom building Coot from source code]].


=Running Coot=
=Running Coot=
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   run_scheme_command("(scheme-command arg1 arg2 ...)")      [from python]
   run_scheme_command("(scheme-command arg1 arg2 ...)")      [from python]
=Enhanced Menu Appearance=
==As of 0.4, coot works with gtk+2==
This permits use of themes for a more OSX-like experience, among other things.
Click on the thumbnail image below to see a full-size screenshot of Coot with a gtk+2 Aqua-like theme.
[[Image:Thumb-coot-gtk2.png]]
To get this effect, you need the Glossy_P gtk+2 theme:
http://art.gnome.org/download/themes/gtk2/571/GTK2-Glossy_P.tar.gz
Edit a file called ~/.gtkrc-2.0 and put into it the following line:
include "/usr/share/themes/Glossy\ P/gtk-2.0/gtkrc"
Alternatively, if you use gnome or xfce4, you can open the theme manager and just make it open the downloaded Glossy_P tarball, and it should add this as a theme.


=Assorted questions and answers (from the mailinglist)=
=Assorted questions and answers (from the mailinglist)=
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Q: Is it possible to deactivate the nomenclature errors check? Sometimes this check is not very useful and it becomes rather annoying when one has several molecules loaded only wants to look at the structures...
Q: Is it possible to deactivate the nomenclature errors check? Sometimes this check is not very useful and it becomes rather annoying when one has several molecules loaded only wants to look at the structures...


A: The [https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#set_002dnomenclature_002derrors_002don_002dread Coot manual] should help: Add to your ~/.coot or whatever:
A: The [https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#set_002dnomenclature_002derrors_002don_002dread Coot manual] should help: Add to your startup script ~/.coot :
  (set-nomenclature-errors-on-read "ignore")
  (set-nomenclature-errors-on-read "ignore")
In case you are using the python file, e.g. “.coot.py”, I think you have to change this to “set_nomenclature_errors_on_read ignore”.
In case you are using the python file ~/.coot.py , use
set_nomenclature_errors_on_read("ignore")
 
On Windows, this line should go into X:\YourWinCootDirectory\.coot-preferences\coot.py .
Alternatively put ".coot.py" in X:\YourWinCootDirectory.


==NCS edits==  
==NCS edits==  
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  set_show_intermediate_atoms_rama_markup(1)
  set_show_intermediate_atoms_rama_markup(1)
  set_do_coot_probe_dots_during_refine(1)
  set_do_coot_probe_dots_during_refine(1)
=See also=
[https://www.youtube.com/watch?v=Xhonm4K1y0c This video] is one of what will be a series of videos showcasing Coot 1 - and this one starts at the beginning.
Kay
Bureaucrats
1,328

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