Coot: Difference between revisions

Coot (edit)

Revision as of 13:09, 15 May 2021

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 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=
@@ Line 12: / Line 13: @@
 ==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.
 ==Installing Coot on Linux==
@@ Line 19: / Line 20: @@
 === 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 http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-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.
-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). If you prefer a "stable" binary, these are at http://www.ysbl.york.ac.uk/~emsley/software/binaries/stable/.
+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 $HOME), and establish a symlink (ln -s) between /usr/local/bin/coot and the bin/coot of the freshly unpacked distribution.
@@ Line 78: / Line 79: @@
 === Installation from source code via autobuild scripts ===
-Installation of coot and all of its dependencies are handled automatically through the autobuild scripts. There are two versions:
+Go to https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/build-install-coot-from-scratch.html
-* [http://www.ysbl.york.ac.uk/~emsley/build-logs/build-it GTK1] - the old user interface. This script builds coot and all its dependencies.
-* [http://www.ysbl.york.ac.uk/~emsley/build-logs/build-it-gtk2-simple GTK2] - the new user interface. This script builds coot and most of the dependencies, excluding GTK2.
-To build Coot, all you should need to do is edit a few settings in the top of the build script, or alternatively specify those settings as environment variables. For example, the following sequence of instructions will build the latest pre-release of the GTK 2 version with python support:
- wget http://www.ysbl.york.ac.uk/~emsley/build-logs/build-it-gtk2-simple
- export AUTOBUILD_INSTALLED=${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=
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   (set-display-lists-for-maps 0)
-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
+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 ====
@@ Line 337: / Line 316: @@
 [[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==
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       pass
-(Eugene Osipov on 22/04/2020 14:43)
+(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)

Coot: Difference between revisions

Coot (edit)

Revision as of 13:09, 15 May 2021

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