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Coot: Difference between revisions
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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]. There's also Paul Emsley's [https://pemsley.github.io/coot/ coot blog]. | ||
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. | |||
=Installing Coot= | =Installing Coot= | ||
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==Installing Coot on Windows== | ==Installing Coot on Windows== | ||
Please refer to [ | Please refer to [http://bernhardcl.github.io/coot/ Bernhard Lohkamp's WinCoot download] page. | ||
==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 | 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 | In short, just go to https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/ and pick a suitable binary, e.g. | ||
coot-0. | coot-0.9.4.1-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz for a Red Hat Enterprise Linux 7 (or CentOS-7) or newer system. | ||
Then un-tar it under /usr/local/src (or in your $HOME), and establish a symlink (ln -s) between /usr/local/bin/coot and the bin/coot of the freshly unpacked distribution. | Then un-tar it under /usr/local/src (or in your $HOME), and establish a symlink (ln -s) between /usr/local/bin/coot and the bin/coot of the freshly unpacked distribution. | ||
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=== Installation from source code via autobuild scripts === | === Installation from source code via autobuild scripts === | ||
Go to https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/build-install-coot-from-scratch.html | |||
=Running Coot= | =Running Coot= | ||
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set_hardware_stereo_angle_factor(0.5) # for the Python fans | set_hardware_stereo_angle_factor(0.5) # for the Python fans | ||
Hardware stereo failure: try | Hardware stereo failure: try the line | ||
(set-display-lists-for-maps 0) | (set-display-lists-for-maps 0) | ||
in coot 0.9 - see https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind2002&L=COOT&P=R312 | |||
in ~/.coot for coot 0.9 - see https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind2002&L=COOT&P=R312 and https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=COOT;49fa8d15.2006 | |||
==== Zalman Stereo ==== | ==== Zalman Stereo ==== | ||
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[[ensemble_plugin.py]] | [[ensemble_plugin.py]] | ||
===Example 6: some basic scripting=== | |||
Q: I want to prepare scripts to run coot functions like water picking or rotamer fitting in command line. Therefore I am looking for some examples of simple coot scripts, e.g. load ref.pdb, load ref.mtz, fft create map. | |||
Answer: | |||
<pre> | |||
imol = read_pdb("6vw1.pdb") | |||
imol_map = make_and_draw_map("6vw1/6vw1_refine.mtz", "2FOFCWT", "PH2FOFCWT", "", 0, 0) | |||
find_waters(imol_map, imol, 0, 1.4, 1) | |||
</pre> | |||
==Python to Scheme and return== | ==Python to Scheme and return== | ||
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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: 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 ~/.coot or whatever: | ||
(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, e.g. “.coot.py”, I think you have to change this to “set_nomenclature_errors_on_read ignore”. | ||
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pass | pass | ||
(Eugene Osipov on 22/04/2020 | (Eugene Osipov on 22/04/2020) | ||
== how to enable the interactive dots during RS refinement and the Ramachandran polyeders? == | |||
(asked by Clemens Grimm on 08/10/2020 ) | |||
A: | |||
set_show_intermediate_atoms_rota_markup(1) | |||
set_show_intermediate_atoms_rama_markup(1) | |||
set_do_coot_probe_dots_during_refine(1) | |||