Coot Download Mac
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Coot is a toolkit for Macromolecular Crystallography and model-building.Coot uses widgets (with the gui builder glade), mmdb, clipper, and OpenGL, together with a new approach to map contouring and importing/creation and other modelling and building operations. Linux and Mac OS X. Download JLigand.jar into a directory. A new link and composite ligand (JLigand, Refmac, Coot) Metal-containing ligand (JLigand) NB.
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Coot is a graphics program for building, refining and analysing macromolecular models obtained with crystallographic procedures.
There is a homepage with extensive documentation. The program may be downloaded for Linux and Windows computers from the primary server. The license of Coot is GNU GPL.
*1Installing Coot
*1.3Installing Coot on Linux
*1.3.1Installation from a distributed binary tarball package
*2Running Coot
*2.1General Topics
*2.1.2Stereographic Display
*2.1.4External Links
*2.2Scheme Scripts
*2.3Python Scripts
*2.4Python to Scheme and return
*2.4.1Translating between Python and Scheme
*3Enhanced Menu Appearance
*4Assorted questions and answers (from the mailinglist)Installing Coot on OS X[edit]
OS X install packages for nightly builds that work on 10.8.X and 10.9.X are available here: Coot OS X package installers
Please refer to the Installing Coot on OS X pageInstalling Coot on Windows[edit]
Please refer to Bernhard Lohkamp’s WinCoot download page.Installing Coot on Linux[edit]
Installing coot on linux is rather more straightforward than on OS X, because most linux systems are based on gnome and/or kde, and tend to have many of the required components already installed. Most of the other dependencies are also readily available.Installation from a distributed binary tarball package[edit]
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) Coot FAQ to find ’Additional Notes’ for your operating system.
In short, just go to http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-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 Download Linux
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.
If you then run coot, and the loader complains that a certain library is missing, just ask
and install the library, again using yum (assuming yum is available in your distribution, otherwise use apt or whatever is there for this purpose).Example: installing a 64bit nightly CentOS5 binary build on 64bit SL6.1[edit]
First of all, SL (Scientific Linux) is a derivative of RHEL, as is CentOS. So all three OSs behave exactly the same.The binaries with ’x86_64’ binaries are for 64bit systems; the ’i386’ binaries are for 32bit systems. Since my notebook is 64bits (’uname -a’ reports ’x86_64’ more than once), I download coot-0.7-pre-1-revision-3999-binary-Linux-x86_64-centos-5-python-gtk2.tar.gz. As root, I ’cd /usr/local/src’ and un-tar. Next, have to find out which libraries are missing. This can be achieved by (note the use of LD_LIBRARY_PATH in the second command - do not permanently modify LD_LIBRARY_PATH !):
So only two libraries are missing! Either they can be installed using yum, or they are already available, but have a higher version.
*First possibility: find out about installable RPM packages (preferred way):Now don’t just install the openssl098e-0.9.8e-17.el6.i686 and its dependencies - it is a 32bit library (the name ends with ’.i686’)! Installing it does not solve the problem - we need a 64bit library. Unfortunately ’yum provides’ does not tell us about the 64bit library (is that a yum bug?). By specifying just the package name (openssl098e.x86_64 would also work, and would avoid any 32bit package)we install both libssl.so.6 and libcrypto.so.6 in their 64bit versions - done!
*Second possibility: find out if the system already has a higher version of the two libraries:So the answer is: there is /usr/lib64/libssl.so which is at version 10, which is compatible with the version we need (6). For libcrypto.so the same is true. So justThe way these symlinks are made they would even work if RHEL upgrades libssl or libcrypto to higher versions. Works for me.
Final step (this does not need to be repeated for a new coot version): create /usr/local/bin/coot with
and make it executable with Installation from source code via autobuild scripts[edit]
Installation of coot and all of its dependencies are handled automatically through the autobuild scripts. There are two versions:
*GTK1 - the old user interface. This script builds coot and all its dependencies.
*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:
(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[edit]
There are also instructions for Custom building Coot from source code.General Topics[edit]Controls[edit]
Stereographic Display[edit]
Coot has several options for stereographic display, ranging from cross-eyed and wall-eyed split-screen stereo, to hardware-stereo modes that work with CRT systems and most recently the new Zalman 3-D LCD monitor.Side-by-Side[edit]
Either cross-eyed or wall-eyed split-screen stereo mode can be invoked using the ’Stereo’ menu item under ’Draw’, as is shown in the image below:Hardware Stereo[edit]
Similarly, hardware stereo can be invoked (assuming you have the CRT, correct graphics card, emitter, etc) using the same menu item, by selecting ’Hardware Stereo’.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.
Hardware stereo failure: try the line
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;49fa8d15.2006Zalman Stereo[edit]
The first viable LCD monitor for stereographics display is made by Zalman and costs about $300: Zalman ZM-M220W
The attributes for this monitor have been tested and described rather extensively by Warren DeLano on the PyMOL site. Please read it for important details and suggested purchasing sources.
The coot zalman page describes specifically how to get this to work with coot on Mac OS X, but the instructions should be generalizable to linux and Windoze.
Note that the stereo effect is very sensitive to the vertical position of your eyes relative to the screen: if you don’t see stereo, try tilting the screen.Stereo: left/right (and front/back) interchanged?[edit]
Establish an additional toolbutton ’swap stereo’:
Main Toolbar -> right mouse click-> Manage buttons-> select Swap Stereo
Or for the script minded:
switch_stereo_sides()
This will toggle the stereo images left and right.External Links[edit]On-line User Manual[edit]Coot’s home page[edit]Current mailing list archives[edit]Scheme Scripts[edit]
Coot can be scripted in scheme (guile) or python - support for each is more or less equal these days.
Several examples of coot extensions to the language can be seen by examining the 0-coot-state.scm file that coot leaves behind when it finishes.COOPS[edit]
Coops generates a coot script from the output of molprobity, specifically probe, reduce, cluster and clashlist.
For an explanation of the principals underlying reduce and clashlist see the Dots Page. Get Molprobity software here.
Use Coot version 0.1 or higher.
Invoke like this (from the directory in which you run coot):
The use Calculate->Scripting to read in and run coops.scm
Get COOPS here.Example Scheme Script 1: Move to Molecule Centres[edit]
This example can be found in the coot scheme sources (the function name is molecule-centres-gui and is in the xxx/share/coot/scheme/coot-gui.scm file). It is a simple function that creates a button box - a button for each coordinates molecule in Coot. It is annotated. Reproduced as coot-scheme1.Example Scheme Script 2: Demo a Few of Coot’s Features[edit]
This is a composite script and demonstrate reading pdb file, an MTZ file, translations, zoom, spin zooms, contour level changing, map masking, real space refinement, water addition and loop fitting.
The data files used in the example can be obtained here and here. Put them in the directory where you start coot. Save the script to your disk, then use Calculate -> Run Script.. to activate it.Example Scheme Script 3: Read CNS data[edit]
This CNS data reading script is a Cootenization of the CN2COOT script written by Joel Bard (it is based on his csh script) and can be used to compare and contrast scheme programming and shell script programming (the coot version is longer to some extent because it does extra error checking).
As well as doing the conversion the resulting mtz/maps are loaded into Coot.
It is part of Coot as of version 0.1.2.Example Scheme Script 4: Load the Latest Data and PDB files Automatically[edit]
To load the most recent files, do this:
which enables the scripting function: (load-latest-files)
For extra gui goodness (you will need 0.1.2): Example Scheme Script 5: Saving a Partial model[edit]
Here we create a small function to save part of a molecule and add a gui interface, it can be used in the usual way (i.e. with --script on the command line, Calculate->Run Script.. or add the script to your ~/.coot file.Example Scheme Script 6: Creating an interface for the Powermate Dial[edit]
The Powermate dial can be used with coot. One could just assign the rotations to +/-y keys and be done with it, but this script gives you a way of having positive and negative rotations in all three cartesian directions. The F1 key is mapped to positive rotation, the F2 key to negative rotation, and the F3 key permits you to toggle through x, y, and z, on successive key presses. I then map F1 and F2 into the ordinary rotations on the powermate (using send key equivalents) and then I map F3 into the single click on the dial, making it easy to toggle through x, y and z. The press-and-rotate options remain available; I map these into scroll up and down, and put them on the slowest response setting, which makes contouring density easier to control than it is from my mouse scroll wheel.Example Scheme Script 7: Applying arbitrary value to ’B’ factor column[edit]
Imagine you have a file of some property (Chemical Shifts, for example) of a residue that you wish to apply to theatoms of a particular model from a pdb file as pseudo B factors. Here’s how to do that in Coot:
We have a file ’cs.tab’ like this, the residue number then the chemical shift value (one for each residue in a particular chain):
1 1.53159
2 4.35884
3 4.07123
4 4.16932
5 6.69103
6 7.12071
7 10.7419
8 9.57176
Use apply-cs.scm to apply these values as pseudo temperature factors. Typical usage, where ’A’ is the chain id, and cs.tab the file of values per residue.
(apply-cs (read-pdb ’test.pdb’) ’A’ ’cs.tab’)
Example Script 8: Partial Occupancy Dialog[edit]
Imagine that you have a structure that has residues with partial occupancy. After refinement, it would be convenient to quickly navigate to all such residues. How can that be done?
Start coot with command line arguments:
This will provide an extra menu item called ’Extras’, clicking on ’Residues with low occupancy..’ therein will lead you through the process.Note that this will often work with SHELXL molecules, because they have atoms with negative (e.g -31) occupancies.
Note also that you will need a recent version of Coot to use this, as it stands. This will not work on stock Coot version 0.4.x. You can enable this for use with 0.4.x if you update/replace your xxx/share/coot/scheme/coot-gui.scm file from here.Example Script 9: A GUI for Chopping Back Sidechains from a Residue Range[edit]
This is a simple interface to the delete-sidechain-range function, it illustrates how arguments can be transferedfrom the GUI to the scripting function. It was written in response to a question from Byron DeLaBarre.
Unfortunately (prior to 0.5) there was an error in the standard delete-sidechain-range function, which is why we over-ride it.Example 10: How do I bind a key to Toggle the display of NCS ghosts?[edit]
With this script: toggle-ncs-ghosts-scriptExample 11: Paul Emsley’s Key Bindings[edit]
Just so you get an idea of the customization by key bindings here are what Paul uses currently (add to your .coot file).Optional Wrappers and (External) Shell Script Enhancements[edit]
I (wgscott) wrote a coot wrapper shell script that lets you convert xplor/cns maps on the fly (you need to install mapman first) and has a few other enhancements.
I also made a Coot OS X applet that allows you to drag and drop a cns/xplor or ccp4 mapfile or any other coot-compatable file (mtz or pdb file, for example). Using the File > Get Info dialog, you can program this applet to open all .map and all .mtz files, if you want to, making these files double-clickable.
Download the Applet (requires a separate working coot installation)Python Scripts[edit]Example 1: Bernhard Lohkamp’s Key Bindings[edit]
Just so you get an idea of the customization by key bindings here are what Bernhard/Paul uses currently (add to your .coot file or put the file in .coot-preferences directory).Example 2: More key bindings (inspired by the Coot BB)[edit]
For (re-)colouring maps blue:
To (re-)colour coordinate molecules yellow:Example 3: NCS Rotamer differences[edit]
To show NCS where NCS-related side-chains have different rotamers:Example 4: Morphing GUI[edit]
GUI to easily access jiggle fit and morphing (currently pre-release Coot required, may be moved into trunk):Example 5: Ensemble GUI[edit]
GUI to allow navigation through structural ensembles as obtained e.g. from ensemble refinement:Python to Scheme and return[edit]Translating between Python and Scheme[edit]
Python scripting is different to (default) scheme scripting which is mainly described in Paul Emsley’s documentation (although it’s mentioned somewhere, fairly hidden). You have to change the commands in the following way:Simple rules for Scheme to Python translations[edit]
Here some simple rules how to translate from Scheme to Python. To translate the other way around, i.e. Python to Scheme, just turn the rules around:
*Replace all ’-’ with ’_’ (except in equation when you need arithmetic ’-’ minus signs)
*Move the brackets around the argument(s)
*Separate multiple arguments by commas rather than spaces
*Replace ’define’ with ’def’ for functions and with ’=’ for assignments
*Make sure to use indentation for the function content [Python is indentation sensitive] and a ’:’ after the function definition.
Some additional/advanced(?) rules:
*#f -> False
*#t -> True
*(set! variable value) -> variable=valueA simple example[edit]
In Scheme we may have the following script:
Which will translate into Python:Running a Scheme/Python command from Python/Scheme[edit]
As of Coot 0.5 (and if you have both scripting languages available) you an use the following commands to run a script or command in the other language:As of 0.4, coot works with gtk+2[edit]
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.
To get this effect, you need the Glossy_P gtk+2 theme:
Edit a file called ~/.gtkrc-2.0 and put into it the following line:
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.
It should be noted that the answers (’A’) are from Paul Emsley himself (and were maybe slightly edited).Coot development[edit]
Q: How can I get involved with Coot development?
A: Join the Coot Janitors project. This is a project to get new people involved in improving Coot, by acting as a clearing house for simple tasks which need doing, and providing documentation for doing them.
Download logo design studio pro mac.Get rid of the ’fix nomenclature’ check[edit]
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 Coot manual should help: Add to your ~/.coot or whatever:
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[edit]
Q: I am sure this exists somewhere through scripting in COOT, but can I apply NCS edits to only a subset of NCS copies? In other words, can I tell coot which are NCS related chains, and which aren’t. I am working on this nightmarish case of asymmetrical homodimers, where the sequences are very similar, but the structures are not, so I need to tell coot which chains are actually related to each other.
A: Nightmare. If you have a recent [1632 or later for the scheme version, 1646 for the python version] Coot, you can do this:
(manual-ncs-ghosts imol resno-start resno-end chain-id-list)
where
*imol is 0 (say)
*resno-start and resno-end is the residue range for the LSQ fitting to return the NCS matrix,
*chain-id-list is the list of chain-ids, starting with the master/reference chain-id and followed by the peer chain-ids that are NCS related, e.g. (list ’A’ ’B’ ’D’)
The python interface is similar.
There is also a GUI to activate this feature under Extensions -> NCS.SHELXL[edit]
Description of problematic situation: I am using SHELXL to refine my 1.2 Å data and I am refining the hydrogen atoms. Subsequent rebuilding in coot is difficult though since hydrogens often does not ’follow’ when you do side chain rebuilding. For the moment I have quit transfering hydrogens to coot and add the hydrogens every refinement cycle, though it would be good I think if I could see them in
https://diarynote.indered.space
Coot is a toolkit for Macromolecular Crystallography and model-building.Coot uses widgets (with the gui builder glade), mmdb, clipper, and OpenGL, together with a new approach to map contouring and importing/creation and other modelling and building operations. Linux and Mac OS X. Download JLigand.jar into a directory. A new link and composite ligand (JLigand, Refmac, Coot) Metal-containing ligand (JLigand) NB.
*Coot Download Linux
*Coot Crystallography Download Mac
*Coot Crystallography Mac
*Coot Model Building
*Coot For Linux
*Coot Linux Install25%
Coot is a graphics program for building, refining and analysing macromolecular models obtained with crystallographic procedures.
There is a homepage with extensive documentation. The program may be downloaded for Linux and Windows computers from the primary server. The license of Coot is GNU GPL.
*1Installing Coot
*1.3Installing Coot on Linux
*1.3.1Installation from a distributed binary tarball package
*2Running Coot
*2.1General Topics
*2.1.2Stereographic Display
*2.1.4External Links
*2.2Scheme Scripts
*2.3Python Scripts
*2.4Python to Scheme and return
*2.4.1Translating between Python and Scheme
*3Enhanced Menu Appearance
*4Assorted questions and answers (from the mailinglist)Installing Coot on OS X[edit]
OS X install packages for nightly builds that work on 10.8.X and 10.9.X are available here: Coot OS X package installers
Please refer to the Installing Coot on OS X pageInstalling Coot on Windows[edit]
Please refer to Bernhard Lohkamp’s WinCoot download page.Installing Coot on Linux[edit]
Installing coot on linux is rather more straightforward than on OS X, because most linux systems are based on gnome and/or kde, and tend to have many of the required components already installed. Most of the other dependencies are also readily available.Installation from a distributed binary tarball package[edit]
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) Coot FAQ to find ’Additional Notes’ for your operating system.
In short, just go to http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-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 Download Linux
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.
If you then run coot, and the loader complains that a certain library is missing, just ask
and install the library, again using yum (assuming yum is available in your distribution, otherwise use apt or whatever is there for this purpose).Example: installing a 64bit nightly CentOS5 binary build on 64bit SL6.1[edit]
First of all, SL (Scientific Linux) is a derivative of RHEL, as is CentOS. So all three OSs behave exactly the same.The binaries with ’x86_64’ binaries are for 64bit systems; the ’i386’ binaries are for 32bit systems. Since my notebook is 64bits (’uname -a’ reports ’x86_64’ more than once), I download coot-0.7-pre-1-revision-3999-binary-Linux-x86_64-centos-5-python-gtk2.tar.gz. As root, I ’cd /usr/local/src’ and un-tar. Next, have to find out which libraries are missing. This can be achieved by (note the use of LD_LIBRARY_PATH in the second command - do not permanently modify LD_LIBRARY_PATH !):
So only two libraries are missing! Either they can be installed using yum, or they are already available, but have a higher version.
*First possibility: find out about installable RPM packages (preferred way):Now don’t just install the openssl098e-0.9.8e-17.el6.i686 and its dependencies - it is a 32bit library (the name ends with ’.i686’)! Installing it does not solve the problem - we need a 64bit library. Unfortunately ’yum provides’ does not tell us about the 64bit library (is that a yum bug?). By specifying just the package name (openssl098e.x86_64 would also work, and would avoid any 32bit package)we install both libssl.so.6 and libcrypto.so.6 in their 64bit versions - done!
*Second possibility: find out if the system already has a higher version of the two libraries:So the answer is: there is /usr/lib64/libssl.so which is at version 10, which is compatible with the version we need (6). For libcrypto.so the same is true. So justThe way these symlinks are made they would even work if RHEL upgrades libssl or libcrypto to higher versions. Works for me.
Final step (this does not need to be repeated for a new coot version): create /usr/local/bin/coot with
and make it executable with Installation from source code via autobuild scripts[edit]
Installation of coot and all of its dependencies are handled automatically through the autobuild scripts. There are two versions:
*GTK1 - the old user interface. This script builds coot and all its dependencies.
*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:
(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[edit]
There are also instructions for Custom building Coot from source code.General Topics[edit]Controls[edit]
Stereographic Display[edit]
Coot has several options for stereographic display, ranging from cross-eyed and wall-eyed split-screen stereo, to hardware-stereo modes that work with CRT systems and most recently the new Zalman 3-D LCD monitor.Side-by-Side[edit]
Either cross-eyed or wall-eyed split-screen stereo mode can be invoked using the ’Stereo’ menu item under ’Draw’, as is shown in the image below:Hardware Stereo[edit]
Similarly, hardware stereo can be invoked (assuming you have the CRT, correct graphics card, emitter, etc) using the same menu item, by selecting ’Hardware Stereo’.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.
Hardware stereo failure: try the line
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;49fa8d15.2006Zalman Stereo[edit]
The first viable LCD monitor for stereographics display is made by Zalman and costs about $300: Zalman ZM-M220W
The attributes for this monitor have been tested and described rather extensively by Warren DeLano on the PyMOL site. Please read it for important details and suggested purchasing sources.
The coot zalman page describes specifically how to get this to work with coot on Mac OS X, but the instructions should be generalizable to linux and Windoze.
Note that the stereo effect is very sensitive to the vertical position of your eyes relative to the screen: if you don’t see stereo, try tilting the screen.Stereo: left/right (and front/back) interchanged?[edit]
Establish an additional toolbutton ’swap stereo’:
Main Toolbar -> right mouse click-> Manage buttons-> select Swap Stereo
Or for the script minded:
switch_stereo_sides()
This will toggle the stereo images left and right.External Links[edit]On-line User Manual[edit]Coot’s home page[edit]Current mailing list archives[edit]Scheme Scripts[edit]
Coot can be scripted in scheme (guile) or python - support for each is more or less equal these days.
Several examples of coot extensions to the language can be seen by examining the 0-coot-state.scm file that coot leaves behind when it finishes.COOPS[edit]
Coops generates a coot script from the output of molprobity, specifically probe, reduce, cluster and clashlist.
For an explanation of the principals underlying reduce and clashlist see the Dots Page. Get Molprobity software here.
Use Coot version 0.1 or higher.
Invoke like this (from the directory in which you run coot):
The use Calculate->Scripting to read in and run coops.scm
Get COOPS here.Example Scheme Script 1: Move to Molecule Centres[edit]
This example can be found in the coot scheme sources (the function name is molecule-centres-gui and is in the xxx/share/coot/scheme/coot-gui.scm file). It is a simple function that creates a button box - a button for each coordinates molecule in Coot. It is annotated. Reproduced as coot-scheme1.Example Scheme Script 2: Demo a Few of Coot’s Features[edit]
This is a composite script and demonstrate reading pdb file, an MTZ file, translations, zoom, spin zooms, contour level changing, map masking, real space refinement, water addition and loop fitting.
The data files used in the example can be obtained here and here. Put them in the directory where you start coot. Save the script to your disk, then use Calculate -> Run Script.. to activate it.Example Scheme Script 3: Read CNS data[edit]
This CNS data reading script is a Cootenization of the CN2COOT script written by Joel Bard (it is based on his csh script) and can be used to compare and contrast scheme programming and shell script programming (the coot version is longer to some extent because it does extra error checking).
As well as doing the conversion the resulting mtz/maps are loaded into Coot.
It is part of Coot as of version 0.1.2.Example Scheme Script 4: Load the Latest Data and PDB files Automatically[edit]
To load the most recent files, do this:
which enables the scripting function: (load-latest-files)
For extra gui goodness (you will need 0.1.2): Example Scheme Script 5: Saving a Partial model[edit]
Here we create a small function to save part of a molecule and add a gui interface, it can be used in the usual way (i.e. with --script on the command line, Calculate->Run Script.. or add the script to your ~/.coot file.Example Scheme Script 6: Creating an interface for the Powermate Dial[edit]
The Powermate dial can be used with coot. One could just assign the rotations to +/-y keys and be done with it, but this script gives you a way of having positive and negative rotations in all three cartesian directions. The F1 key is mapped to positive rotation, the F2 key to negative rotation, and the F3 key permits you to toggle through x, y, and z, on successive key presses. I then map F1 and F2 into the ordinary rotations on the powermate (using send key equivalents) and then I map F3 into the single click on the dial, making it easy to toggle through x, y and z. The press-and-rotate options remain available; I map these into scroll up and down, and put them on the slowest response setting, which makes contouring density easier to control than it is from my mouse scroll wheel.Example Scheme Script 7: Applying arbitrary value to ’B’ factor column[edit]
Imagine you have a file of some property (Chemical Shifts, for example) of a residue that you wish to apply to theatoms of a particular model from a pdb file as pseudo B factors. Here’s how to do that in Coot:
We have a file ’cs.tab’ like this, the residue number then the chemical shift value (one for each residue in a particular chain):
1 1.53159
2 4.35884
3 4.07123
4 4.16932
5 6.69103
6 7.12071
7 10.7419
8 9.57176
Use apply-cs.scm to apply these values as pseudo temperature factors. Typical usage, where ’A’ is the chain id, and cs.tab the file of values per residue.
(apply-cs (read-pdb ’test.pdb’) ’A’ ’cs.tab’)
Example Script 8: Partial Occupancy Dialog[edit]
Imagine that you have a structure that has residues with partial occupancy. After refinement, it would be convenient to quickly navigate to all such residues. How can that be done?
Start coot with command line arguments:
This will provide an extra menu item called ’Extras’, clicking on ’Residues with low occupancy..’ therein will lead you through the process.Note that this will often work with SHELXL molecules, because they have atoms with negative (e.g -31) occupancies.
Note also that you will need a recent version of Coot to use this, as it stands. This will not work on stock Coot version 0.4.x. You can enable this for use with 0.4.x if you update/replace your xxx/share/coot/scheme/coot-gui.scm file from here.Example Script 9: A GUI for Chopping Back Sidechains from a Residue Range[edit]
This is a simple interface to the delete-sidechain-range function, it illustrates how arguments can be transferedfrom the GUI to the scripting function. It was written in response to a question from Byron DeLaBarre.
Unfortunately (prior to 0.5) there was an error in the standard delete-sidechain-range function, which is why we over-ride it.Example 10: How do I bind a key to Toggle the display of NCS ghosts?[edit]
With this script: toggle-ncs-ghosts-scriptExample 11: Paul Emsley’s Key Bindings[edit]
Just so you get an idea of the customization by key bindings here are what Paul uses currently (add to your .coot file).Optional Wrappers and (External) Shell Script Enhancements[edit]
I (wgscott) wrote a coot wrapper shell script that lets you convert xplor/cns maps on the fly (you need to install mapman first) and has a few other enhancements.
I also made a Coot OS X applet that allows you to drag and drop a cns/xplor or ccp4 mapfile or any other coot-compatable file (mtz or pdb file, for example). Using the File > Get Info dialog, you can program this applet to open all .map and all .mtz files, if you want to, making these files double-clickable.
Download the Applet (requires a separate working coot installation)Python Scripts[edit]Example 1: Bernhard Lohkamp’s Key Bindings[edit]
Just so you get an idea of the customization by key bindings here are what Bernhard/Paul uses currently (add to your .coot file or put the file in .coot-preferences directory).Example 2: More key bindings (inspired by the Coot BB)[edit]
For (re-)colouring maps blue:
To (re-)colour coordinate molecules yellow:Example 3: NCS Rotamer differences[edit]
To show NCS where NCS-related side-chains have different rotamers:Example 4: Morphing GUI[edit]
GUI to easily access jiggle fit and morphing (currently pre-release Coot required, may be moved into trunk):Example 5: Ensemble GUI[edit]
GUI to allow navigation through structural ensembles as obtained e.g. from ensemble refinement:Python to Scheme and return[edit]Translating between Python and Scheme[edit]
Python scripting is different to (default) scheme scripting which is mainly described in Paul Emsley’s documentation (although it’s mentioned somewhere, fairly hidden). You have to change the commands in the following way:Simple rules for Scheme to Python translations[edit]
Here some simple rules how to translate from Scheme to Python. To translate the other way around, i.e. Python to Scheme, just turn the rules around:
*Replace all ’-’ with ’_’ (except in equation when you need arithmetic ’-’ minus signs)
*Move the brackets around the argument(s)
*Separate multiple arguments by commas rather than spaces
*Replace ’define’ with ’def’ for functions and with ’=’ for assignments
*Make sure to use indentation for the function content [Python is indentation sensitive] and a ’:’ after the function definition.
Some additional/advanced(?) rules:
*#f -> False
*#t -> True
*(set! variable value) -> variable=valueA simple example[edit]
In Scheme we may have the following script:
Which will translate into Python:Running a Scheme/Python command from Python/Scheme[edit]
As of Coot 0.5 (and if you have both scripting languages available) you an use the following commands to run a script or command in the other language:As of 0.4, coot works with gtk+2[edit]
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.
To get this effect, you need the Glossy_P gtk+2 theme:
Edit a file called ~/.gtkrc-2.0 and put into it the following line:
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.
It should be noted that the answers (’A’) are from Paul Emsley himself (and were maybe slightly edited).Coot development[edit]
Q: How can I get involved with Coot development?
A: Join the Coot Janitors project. This is a project to get new people involved in improving Coot, by acting as a clearing house for simple tasks which need doing, and providing documentation for doing them.
Download logo design studio pro mac.Get rid of the ’fix nomenclature’ check[edit]
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 Coot manual should help: Add to your ~/.coot or whatever:
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[edit]
Q: I am sure this exists somewhere through scripting in COOT, but can I apply NCS edits to only a subset of NCS copies? In other words, can I tell coot which are NCS related chains, and which aren’t. I am working on this nightmarish case of asymmetrical homodimers, where the sequences are very similar, but the structures are not, so I need to tell coot which chains are actually related to each other.
A: Nightmare. If you have a recent [1632 or later for the scheme version, 1646 for the python version] Coot, you can do this:
(manual-ncs-ghosts imol resno-start resno-end chain-id-list)
where
*imol is 0 (say)
*resno-start and resno-end is the residue range for the LSQ fitting to return the NCS matrix,
*chain-id-list is the list of chain-ids, starting with the master/reference chain-id and followed by the peer chain-ids that are NCS related, e.g. (list ’A’ ’B’ ’D’)
The python interface is similar.
There is also a GUI to activate this feature under Extensions -> NCS.SHELXL[edit]
Description of problematic situation: I am using SHELXL to refine my 1.2 Å data and I am refining the hydrogen atoms. Subsequent rebuilding in coot is difficult though since hydrogens often does not ’follow’ when you do side chain rebuilding. For the moment I have quit transfering hydrogens to coot and add the hydrogens every refinement cycle, though it would be good I think if I could see them in
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