Coot: Difference between revisions

Coot (edit)

Revision as of 12:09, 15 May 2021

241 bytes added , 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 the [http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot-download.html WinCoot install and 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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 [[Image:a_zalman_zm_m220w__2d_35_pic.jpg|150px|thumb|right|3d lcd]]
+Control stereo separation / depth in coot 0.9: the transformation between the eyes is no longer a rotation and is now a shear. Which means that now we don't get part of the map showing up in the left eye but not the right (or vice versa).
+This is documented in Section 3.4.1, e.g.
+ set_hardware_stereo_angle_factor(0.5) # for the Python fans
+Hardware stereo failure: try the line
+ (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
 ==== Zalman Stereo ====
@@ Line 150: / Line 140: @@
 ===External Links===
-====[http://www.ysbl.york.ac.uk/~emsley/coot/doc/user-manual.html On-line User Manual]====
+====[https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html On-line User Manual]====
-====[http://www.ysbl.york.ac.uk/~emsley/coot/ Coot's home page]====
+====[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.ysbl.york.ac.uk/~emsley/coot/mbox/ Mailing list archives: (no longer) current]====
-====[http://www.ysbl.york.ac.uk/~emsley/coot/mbox-2004-2005/ Mailing list archives: 2004-05]====
 ==Scheme Scripts==
@@ Line 330: / 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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 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")
+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”.
 ==NCS edits==
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 A: Turn up the radius a bit and use (set-symmetry-shift-search-size 3) . I would have thought that 2 is big enough, but maybe not in this case.
+== specify Coot download directory, like specifying backup dir by COOT_BACKUP_DIR? ==
+here is my working startup.py (of course replace src folder with your preferred location):
+ import os
+ try:
+     os.symlink('/ccp4/xray/tmp/', 'coot-download')
+ except:
+     pass
+(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)