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Coot: Difference between revisions
→Installing Coot on Windows
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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/ | 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 [ | 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 | 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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===External Links=== | ===External Links=== | ||
====[ | ====[https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html On-line User Manual]==== | ||
====[ | ====[https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ Coot's home page]==== | ||
====[http://www.mail-archive.com/coot@jiscmail.ac.uk/ Current mailing list archives]==== | ====[http://www.mail-archive.com/coot@jiscmail.ac.uk/ Current mailing list archives]==== | ||
==Scheme Scripts== | ==Scheme Scripts== | ||
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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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run_scheme_command("(scheme-command arg1 arg2 ...)") [from python] | run_scheme_command("(scheme-command arg1 arg2 ...)") [from python] | ||
=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: Add to your ~/.coot | 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 ~/.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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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) | |||
=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. | |||