The Coot User Manual
The Coot User Manual
Table of Contents
Coot User Manual
Concept index.
Function index.
--- The Detailed Node Listing ---
Introduction
Mousing and Keyboarding
General Features
Backups and Undo
Coordinate-Related Features
Modelling and Building
Regularization and Real Space Refinement
Map-Related Features
Validation
Hints and Usage Tips
Other Programs
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1 Introduction
This document is the Coot User Manual, giving an overview of the
interactive features.
Other documentation includes the
Coot Reference Manual and the Coot
These documents should be distributed with
the source code.
1.1 Citing Coot and Friends
If have found this software to be useful, you are requested
(if appropriate) to cite:
"Features and Development of Coot"
P Emsley, B Lohkamp, W Scott, and K Cowtan
Acta Cryst. (2010).
D66, 486-501
Acta Crystallographica Section D-Biological Crystallography
66: 486-501
The reference for the REFMAC5 Dictionary is:
REFMAC5 dictionary: "Organization of Prior Chemical Knowledge and
Guidelines for its Use" Vagin AA, Steiner RA, Lebedev AA, Potterton L,
McNicholas S Long F, Murshudov GN Acta Crystallographica Section
D-Biological Crystallography 60:
Part 12 Sp. Iss. 1
If using "SSM Superposition", please cite:
"Secondary-structure matching (SSM), a new tool for fast
protein structure alignment in three dimensions"
Krissinel E, Henrick K
Acta Crystallographica Section D-Biological Crystallography
Part 12 Sp. Iss. 1 DEC 2004
The reference for the the Electron Density Server is:
GJ Kleywegt, MR Harris, JY Zou, TC Taylor, A W&hlby,
TA Jones (2004),
"The Uppsala Electron-Density Server",
Acta Crystallographica Section D-Biological Crystallography 60, .
Please also cite the primary literature for the received structures.
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1.2 What is Coot?
Coot is a molecular graphics application. Its primary focus is
crystallographic macromolecular model-building and manipulation rather
than representation i.e. more like Frodo than Rasmol.
Having said that, Coot can work with small molecule (SHELXL) and electron
microscopy data, be used for homology modelling, make passably pretty
pictures and display NMR structures.
Coot is Free Software.
You can give it away. If you don't like the way
it behaves, you can fix it yourself.
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1.3 What Coot is Not
Coot is not:
CCP4's official Molecular Graphics program
a program to do refinement
a protein crystallographic suite.
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1.4 Hardware Requirements
The code is designed to be portable to any Unix-like operating system.
Coot certainly runs on SGI IRIX64, RedHat Linux of various sorts, SuSe
and MacOS X (10.2).
Coot binaries should also work on IRIX.
If you want to port to some other operating system, you are welcome
Note that your task will be eased by using GNU GCC to compile
the programs components.
1.4.1 Mouse
Coot works best with a 3-button mouse and works better if
it has a scroll-wheel too (see Chapter 2 for more details) .
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1.5 Environment Variables
Coot responds to several environment variables that modify its
behaviour.
COOT_STANDARD_RESIDUES
The filename of the pdb file
containing the standard amino acid residues in &standard
conformation&
COOT_SCHEME_DIR
The directory containing standard (part of the distribution) scheme
COOT_SCHEME_EXTRAS_DIR
A ':'-separated list of directories containing bespoke scheme files.
This variable is not set by default.
If you set it, Coot will test
each ':'-separated string that it points to a directory, and if it does,
Coot will load all the .scm files in that directory.
COOT_PYTHON_EXTRAS_DIR
A ':'-separated list of directories containing bespoke python files.
This variable is not set by default.
If you set it, Coot will test
each ':'-separated string that it points to a directory, and if it does,
Coot will load all the .py files in that directory.
COOT_REF_STRUCTS
The directory containing a set of high resolution pdb files used as
reference structures to build backbone atoms from
C\alpha positions
COOT_REF_SEC_STRUCTS
The directory containing a set of high-quality structures to be used
as templates for fitting beta strands.
If this is not set, then the
directory COOT_REF_SEC_STRUCTS will be used to find the reference pdb
COOT_REFMAC_LIB_DIR
Refmac's CIF directory containing the monomers and link descriptions.
In the future this may simply be the same directory in which refmac
looks to find the library dictionary.
COOT_SBASE_DIR
The directory to find the SBASE dictionary (often comes with CCP4).
COOT_RESOURCES_DIR
The directory that contains the
splash screen image and the GTK+ application resources.
COOT_BACKUP_DIR
The directory to which backup are
written (if it exists as a directory).
If it is not, then backups
are written to the current directory (the directory in which coot
was started).
And of course extension language environment variables are used too:
PYTHONPATH (for python modules)
GUILE_LOAD_PATH (for guile modules)
Normally, these environment variables will be set correctly in the coot
shell script.
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1.6 Command Line Arguments
Rather that using the GUI to read in information, you can use the
following command line arguments:
--c cmd to run a command cmd on start up
--script filename to run a script on start up (but see Section )
--no-state-script don't run the 0-coot.state.scm script on start up.
Don't save a state script on exit either.
--pdb filename
for pdb/coordinates file
--coords filename
for SHELX .ins/.res and CIF files
--data filename for mtz, phs or mmCIF data file
--auto filename for auto-reading mtz files (mtz file has the default labels FWT, PHWT)
--map filename
for a map (currently CCP4-format only)
--dictionary filename read in a cif monomer dictionary
--help print command line options
--stereo start up in hardware stereo mode
--version print the version of coot and exit
--code accession-code on starting Coot, get the pdb file
and mtz file (if it exists) from the EDS
--no-guano don't leave &Coot droppings& i.e. don't write state
and history files on exit
--side-by-side start in side-by-side stereo mode
--update-self command-line mode to update the coot to the latest
pre-release on the server
--python an argument with no parameters - used to tell Coot that
the -c arguments should be process as python (rather than as scheme).
--small-screen start with smaller icons and font to fit on small
screen displays
--zalman-stereo start in Zalman stereo mode
So, for example, one might use:
coot --pdb post-refinement.pdb --auto refmac-2.mtz --dictionary lig.cif
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1.7 Web Page
Coot has a web page:
There you can read more about the CCP4 molecular graphics project in
general and other projects which are important for Coot .
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Coot might crash on you - it shouldn't.
Whenever Coot manipulates the model, it saves a backup pdb file.
There are backup files in
the directory coot-backup . You can recover the session (until the last
edit) by reading in the pdb file that you started with last time and
then use File -& Recover Session....
I would like to know about coot crashing
so that I can fix it as soon as possible. If you want your
problem fixed, this involves some work on your part sadly.
First please make sure that you are using the most recent version of
I will often need to know as much as possible about what you did
to cause the bug.
If you can reproduce the bug and send me the files
that are needed to cause it, I can almost certainly fix it
- especially if you
use the debugger (gdb) and send a backtrace
Note that you may have to source the
contents of bin/coot so that the libraries are can be found when
the executable dynamically links.
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2 Mousing and Keyboarding
How do we move around and select things?
Left-mouse Drag
Rotate view
Ctrl Left-Mouse Drag
Translates view
Shift Left-Mouse
Label Atom
Right-Mouse Drag
Zoom in and out
Ctrl Shift Right-Mouse Drag
Rotate View around Screen Z axis
Middle-mouse
Centre on atom
Scroll-wheel Forward
Increase map contour level
Scroll-wheel Backward
Decrease map contour level
See also Chapter
for more help.
2.1 Next Residue
Next Residue
``Shift'' ``Space''
Previous Residue
See also &Recentring View& (Section ).
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2.2 Keyboard Contouring
Use &+& or &-& on the keyboard if you don't have a
scroll-wheel.
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2.3 Mouse Z Translation and Clipping
Here we can change the clipping and Translate in Screen Z
Ctrl Right-Mouse Drag Up/Down
changes the slab (clipping planes)
Ctrl Right-Mouse Drag Left/Right
translates the view in screen Z
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2.4 Keyboard Translation
Keypad 3 Push View (+Z translation)
Keypad . Pull View (-Z translation)
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2.5 Keyboard Zoom and Clip
Fatten clip
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2.6 Scrollwheel
When there is no map, using the scroll-wheel has no effect.
is exactly one map displayed,
the scroll-wheel
will change the contour level of that map.
If there are two or more
maps, the map for which the contour level is changed can be set using either
HID -& Scrollwheel -& Attach scroll-wheel
to which map? and selecting a map number or clicking the "Scroll"
radio button for the map in the Display Manager.
You can turn off the map contour level changing by the scroll wheel using:
(set-scroll-by-wheel-mouse 0)
(the default is 1 [on]).
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2.7 Selecting Atoms
Several Coot functions require the selecting of atoms to specify a
residue range (for example: Regularize, Refine (Section
) or Rigid Body Fit Zone (Section
Select atoms with the Left-mouse.
See also Picking (Section ).
Use the scripting function
(quanta-buttons) to make the mouse
functions more like other molecular graphics programs to which you may
be more accustomed .
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2.8 Virtual Trackball
You may not completely like the way the
molecule is moved by the mouse movement .
To change this, try:
HID -& Virtual Trackball -& Flat.
do this from the scripting interface: (vt-surface
If you do want screen-z rotation
screen-z rotation, you can either use Shift Right-Mouse Drag or set
the Virtual Trackball to Spherical Surface mode and move the mouse
along the bottom edge of the screen.
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2.9 More on Zooming
The function (quanta-like-zoom) adds the ability to zoom the
view using just Shift + Mouse movement .
There is also a Zoom slider
(Draw -& Zoom) for those without a right-mouse button.
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3 General Features
The map-fitting and model-building tools can be accessed by using
Calculate -& Model/Fit/Refine....
Many functions have
describing the particular features and are documented in Chapter
posts the Model/Fit/Refine dialog
posts the Go To Atom Window
posts the Display Control Window
3.1 Version number
The version number of Coot can be found at the top of the &About&
window (Help -& About).
This will return the version of coot:
$ coot --version
There is also a script function to return the version of coot:
(coot-version)
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3.2 Antialiasing
The built-in antialiasing (for what it's worth) can be enabled using:
(set-do-anti-aliasing 1)
The default is 0 (off).
This can also be activated using Edit Preferences -& Others -&
Antialiasing -& Yes.
If you have an nVidia graphics card, external antialiasing can be
actived setting the environment variable __GL_FSAA_MODE.
setting of 5 works nicely and gives a better image than using
Coot's built-in antialiasing.
Also for nVidia graphics card users, there is the application
nvidia-settings:
Antialiasing Setting -& Override Application Settings and
slide the slider to the right. On restarting Coot, it should be in
antialias mode .
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3.3 Molecule Number
Coot is based on the concept of molecules.
Maps and coordinates are
different representations of molecules.
The access to the molecule is
via the molecule number.
It is often important therefore to
know the molecule number of a particular molecule.
The Molecule Number of a molecule can be found by clicking on an atom of
that molecule (if it has coordinates of course). The first number in
brackets in the resulting text in the status bar and console is the
Molecule Number.
The Molecule Number can also be found in Display
Control window (Section ).
It is also displayed on
the left-hand side of the molecule name in the option menus of the
&Save Coordinates& and &Go To Atom& windows.
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3.4 Display Issues
The &graphics& window is drawn using
It is considerably smoother (i.e. more frames/sec) when using a
3D accelerated X server.
The view is orthographic (i.e. the back is the same size as the
The default clipping is about right for viewing coordinate
data, but is often a little too &thick& for viewing electron
It is easily changed (see Section ).
Depth-cueing
is linear and fixed on.
The graphics window can be resized, but it has a minimum size of
400x400 pixels.
3.4.1 Stereo
Hardware Stereo is an option for Coot (Draw -& Stereo... -&
Hardware Stereo -& OK), side-by-side stereo is not an option.
The angle between the stereo pairs (the stereo separation) can be
changed to suit your personal tastes using:
(set-hardware-stereo-angle-factor angle-factor)
where angle-factor would typically be between 1.0 and 2.0
3.4.2 Pick Cursor
When asked to pick a residue or atom, the cursor changes from the normal
arrow shape to a "pick" cursor.
Sometimes it is difficult to see the
default pick cursor, so you can change it using the function
(set-pick-cursor-index i)
where i is an integer less than 256.
The cursors can be
viewed using an external X program:
xfd -fn cursor
3.4.3 Origin Marker
A yellow box
called the &origin
marks the origin.
It can be removed using:
(set-show-origin-marker 0)
Its state can be queried like this:
(show-origin-marker-state)
which returns an number (0 if it is not displayed, 1 if it is).
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3.5 Screenshot
A simple screenshot (image dump) can be made using Draw -&
Screenshot -& Simple....
Note that in side by side stereo mode you
only get the left-hand image.
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3.6 Raster3D output
Output suitable for use by Raster3D's
can be generated using the scripting function
(raster3d file-name)
where file-name is such as "test.r3d"
There is a keyboard key to generate this file, run &render& and
display the image: Function key F8.
You can also use the function
(render-image)
which will create a file coot.r3d, from which &render& produces
coot.png. This png file is displayed using ImageMagick's display
program (by default).
Use something like:
(set! coot-png-display-program "gqview")
to change that to different display program ("gqview" in this case).
(set! coot-png-display-program "open")
would use Preview (by default) on Macintosh.
To change the widths of the bonds and density &lines& use (for example):
(set-raster3d-bond-thickness 0.1)
(set-raster3d-density-thickness 0.01)
Similarly for bones:
(set-raster3d-bone-thickness 0.05)
To turn off the representations of the atoms (spheres):
(set-renderer-show-atoms 0)
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3.7 Display Manager
This is also known as &Map and molecule
(coordinates) display control&.
Here you can select which maps and
molecules you can see and how they are drawn .
The &Display& and &Active& are toggle buttons, either
depressed (active) or undepressed (inactive).
The &Display& buttons
control whether a molecule (or map) is drawn and the &Active& button
controls if the molecule is clickable
(i.e. if the molecule's atoms can be labeled).
The "Scroll" radio buttons sets which map is has its contour level
changed by scrolling the mouse scroll wheel.
By default, the path names of the files are not displayed in the
Display Manager.
To turn them on:
(set-show-paths-in-display-manager 1)
If you pull across the
horizontal scrollbar in a Molecule view, you will see the &Render
You can use this to change between normal &Bonds (Colour
by Atom)&,&Bonds (Colour by Chain)& and &C\alpha&
representation
There is also
available &No Waters& and &C\alpha + ligands& representations.
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3.8 The Modelling Toolbar
You might not want to have the right-hand-side vertical toolbar that
contains icons for some modelling operations
displayed:
(hide-modelling-toolbar)
to bring it back again:
(show-modelling-toolbar)
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3.9 The file selector
3.9.1 File-name Filtering
The &Filter& button in the fileselection
filters the filenames according to extension.
For coordinates files
the extensions are &.pdb& &.brk& &.mmcif& and others.
&.mtz&, &.hkl&, &.phs&, &.cif& and for (CCP4) maps &.ext&,
&.msk& and &.map&.
If you want to add to the extensions, the
following functions are available:
(add-coordinates-glob-extension extension)
(add-data-glob-extension extension)
(add-map-glob-extension extension)
(add-dictionary-glob-extension extension)
where extension is something like: ".mycif".
If you want the fileselection to be filtered without having to use the
"Filter" button, use the scripting function
(set-filter-fileselection-filenames 1)
3.9.2 Filename Sorting
If you like your files initially sorted by date (rather than
lexicographically, which is the default) use:
(set-sticky-sort-by-date)
3.9.3 Save Coordinates Directory
Some people prefer that the fileselection for saving coordinates starts
in the original directory (rather than the directory from which they
last imported coordinates).
This option is for them:
(set-save-coordinates-in-original-directory 1)
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3.10 Scripting
There is an compile-time option of adding a script interpreter.
Currently the options are python and guile.
It seems possible that in
future you will be able to use both in the same executable.
The binary
distribution of Coot are linked with guile, others with python.
Hundreds of commands are made available for use in scripting by using
SWIG, some of which are documented here. Other functions documented less
well, but descriptions for them can be found at the end of this manual.
Commands described throughout this manual (such as (vt-surface
1)) can be evaluated
directly by Coot by using the &Scripting Window& (Calculate
-& Scripting...). Note that you type the commands in the upper
entry widget and the command gets echoed (in red) and the return value
and any output is displayed in the text widget lower (green).
command should be terminated with a carriage return .
can be evaluated (executed)
using Calculate -& Run Script....
Note that in scheme (the usual scripting language of Coot), the
parentheses are important.
To execute a script file from the command line use the --script
filename arguments
(except when also using the command line
argument --no-graphics, in which case you should use -s
filename).
After you have used the scripting window, you may have noticed that you
can no longer kill Coot by using Ctrl-C in the console.
To recover this
in the scripting window.
3.10.1 Python
* Python Commands
Coot has an (optional) embedded python interpreter.
Thus the full power of python is available to you.
Coot will look for
an initialization script
($HOME/.coot.py) and
will execute it if found.
This file should contain python commands
that set your personal preferences.
3.10.1.1 Python Commands
The scripting functions described in this manual are formatted
suitable for use with guile, i.e.:
(function arg1 arg2...)
If you are using Python instead: the format needs to be changed to:
function(arg1,arg2...)
Note that dashes in guile function names become underscores for
python, so that (for example) (raster-screen-shot) becomes
raster_screen_shot().
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3.10.2 Scheme
The scheme interpreter is made available by embedding
The initialization script used by this interpreter is
$HOME/.coot.
This file should contain scheme commands that
set your personal preferences.
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3.10.3 Coot State
The &state&
of Coot is saved on Exit and written to a
file called 0-coot.state.scm (scheme)
0-coot.state.py (python).
state file contains information about the screen centre, the
clipping, colour map rotation size, the symmetry radius, and other
molecule related parameters such as filename, column labels,
coordinate filename etc..
Use Calculate -& Run Script... to use this file
to re-create the loaded maps and models that you had when you finished
using Coot
last time.
A state file can be saved at any time using (save-state)
which saves to file 0-coot.state.scm or
(save-state-filename "thing.scm") which saves to file
thing.scm.
When Coot starts it can optionally run the commands in
0-coot.state.scm.
Use (set-run-state-file-status i)
to change the behaviour: i is 0 to never run this
state file at
startup, i is
1 to get a dialog option (this is the default) and i
is 2 to run the commands without question.
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3.10.4 Key Binding
&Power users& of Coot might like to write their own functions and bind
that function to a keyboard key.
How do they do that?
By using the add-key-binding function:
(add-key-binding function-name key function)
where key is a quoted string (note that upper case and
lower case keys are distinguished - activate get upper case key binding
you need to chord the shift key ).
for example:
(add-key-binding "Refine Active Residue with Auto-accept" "x" refine-active-residue)
Have a look at the key bindings section on the Coot wiki for several
more examples.
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3.10.5 User-Defined Functions
&Power users& of Coot might also like to write their own functions
that occur after picking an atom (or a number of atoms)
(user-defined-click n_clicks udfunc)
define a function func which runs after the user has
made n_clicked atom picks.
func is called
with a list of atom specifiers - the first member of which is the
molecule number.
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3.11 Backups and Undo
* Restoring from Backup::
By default, each time a modification is made to a model, the old
coordinates are written out .
The backups are kept in a
backup directory and are tagged with the date and the history number
(lower numbers are more ancient ).
The &Undo& function discards
the current molecule and loads itself from the most recent backup
coordinates.
Thus you do not have to remember to &Save Changes& -
coot will do it for you .
If you have made changes to more than one molecule, Coot will pop-up a
dialog box in which you should set the &Undo Molecule& i.e.
the molecule to which the Undo operations will apply.
Further Undo
operations will continue to apply to this molecule until there are
none left.
If another Undo is requested Coot checks to see if there
are other molecules that can be undone, if there is exactly one, then
that molecule becomes the &Undo Molecule&, if there are more than
one, then another Undo selection dialog will be displayed.
You can set the undo molecule using the scripting function:
(set-undo-molecule imol)
If for reasons of strange system
requirements you want to remove the path components of the backup file
name you can do so using:
(set-unpathed-backup-file-names 1)
3.11.1 Redo
The &undone& modifications can be re-done using this
This is not available immediately after a
modification .
3.11.2 Restoring from Backup
There may be certain
circumstances
in which you
wish to restore from a backup but can't get it by the &Undo&
mechanism described above.
In that case, start coot as normal and
then open the (typically most recent) coordinates file in the
directory coot-backup (or the directory pointed to the
environment variable COOT_BACKUP_DIR if it was set) .
This file should contain your most recent edits.
In such a case, it
is sensible for neatness purposes to immediately save the coordinates
(probably to the current directory) so that you are not modifying a
file in the backup directory.
See also Section .
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3.12 View Matrix
It is sometimes useful to use this to orient the
view and export this orientation to other programs.
The orientation
matrix of the view can be displayed (in the console) using:
(view-matrix)
Also, the internal representation of the view can be returned and set
(view-quaternion) to return a 4-element list
(set-view-quaternion i j k l) which sets the view quaternion.
So the usage of these functions would be something like:
(let ((v (view-quaternion)))
; manipulate v here, maybe
(apply set-view-quaternion v))
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3.13 Space Group and Symmetry
Occasionally you may want to know the space group of a particular
Interactively (for maps) you can see it using the Map
Properties button in the Molecule Display Control dialog.
There is a scripting interface function that returns the space group
for a given molecule
(show-spacegroup imol)
You can force a space group onto a molecule using the following:
(set-space-group imol space-group)
where space-group is one of the standard CCP4 space group
names (e.g. "P 21 21 21").
To show the symmetry operators of a particular molecule use:
(get-symmetry imol)
which will return a list of strings.
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3.14 Recentring View
Use Control + left-mouse to drag around the view
middle-mouse over an atom.
In this case, you will often see
&slide-recentring&, the graphics smoothly changes between the
current centre and the newly selected centre.
Use Draw -& Go To Atom... to select an atom
using the keyboard.
Note that you can subsequently use &Space& in
the &graphics& window (OpenGL canvas) to recentre on the next
To centre on an arbitrary position (x,y,z), use the scripting function
(set-rotation-centre x y z).
Use the keyboard: [Ctrl G] then key in a residue number and (optionally) a chainid
and press Return
If you don't want smooth recentring (sliding)
Edit -& Preferences -& Smooth Recentring -& Off.
can also use this dialog to speed it up a bit (by decreasing the
number of steps instead of turning it off).
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3.15 Views
Coot has a views interface (you might call them &scenes&) that
define a particular orientation, zoom and view centre.
linearly interpolate between the views.
The animation play back speed
can be set with the &Views Play Speed& menu item - default is a
speed of 10.
The views interface can be found under the Extensions menu item.
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3.16 Clipping Manipulation
The clipping planes (a.k.a. &slab&
be adjusted using Edit -& Clipping and adjusting
the slider.
There is only one parameter to change and it affects both
the front and the back clipping planes .
The clipping can also be changed using keyboard &D& and &F&.
It can also be changed with Ctrl + Right-mouse drag up and down.
Likewise the screen-Z can be changed with Ctrl + Right-mouse left and
One can &push& and &pull& the view in the screen-Z direction using
keypad 3 and keypad &.& (see Section ).
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3.17 Background colour
The background colour can be set either using a GUI dialog
(Edit$ -& Background Colour) or the function
(set-background-colour 0.00 0.00 0.00), where the arguments
are 3 numbers between 0.0 and 1.0, which respectively represent the
red, green and blue components of the background colour.
The default
is (0.0, 0.0, 0.0) (black).
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3.18 Unit Cell
If coordinates have symmetry available then unit
cells can be drawn for molecules (Draw -& Cell &
Symmetry -& Show Unit Cell?).
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3.19 Rotation Centre Pointer
There is a pink pointer
at the centre of the screen that marks the rotation centre.
The size of the pointer can be changed using Edit
-& Pink Pointer Size... or using scripting commands:
(set-rotation-centre-size 0.3).
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3.20 Orientation Axes
The green axes showing the orientation of the molecule are displayed
by default.
To remove them use th
(set-draw-axes 0)
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3.21 Pointer Distances
The Rotation Centre Pointer is sometimes called simply &Pointer&.
One can find distances to the pointer from any active set of atoms
using &Pointer Distances& (under Measures).
If you move the Pointer
(e.g. by centering on an atom) and want to update the distances
to it, you have to toggle off and on the &Show Pointer Distances& on
the Pointer Distances dialog.
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3.22 Crosshairs
Crosshairs can be drawn at the centre of the screen, using either the
&C& key in graphics
window or Draw -& Crosshairs....
The ticks are at
1.54&A, 2.7&A and 3.8&A.
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3.23 3D Annotations
Positions in 3D space can be annotated with 3D text.
The mechanism to
do this can be found under Extensions -& Representations -& 3D
Annotations.
3D Annotations can be saved to and loaded from a file.
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3.24 Frame Rate
Sometimes, you might as yourself &how fast is the computer?&
Using Calculate -&
Frames/Sec you can see how fast the molecule is rotating, giving an
indication of graphics performance.
It is often better to use a map
that is more realistic and stop the picture whizzing round.
The output
is written to the status bar and the console, you need to give it a few
seconds to &settle down&.
It is best not to have other widgets
overlaying the GL canvas as you do this.
The contouring elapsed time
gives an indication of CPU performance.
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3.25 Program Output
Due to its &in development& nature (at the moment),
Coot produces a lot of &console&
output - much of it debugging or
&informational&.
This will go away in due course.
You are advised
to run Coot so that you can see the console and the graphics window at
the same time, since feedback from atom clicking (for example) is
often written there rather than displayed in the graphics window.
Output that starts &ERROR...& is a programming problem (and
ideally, you should never see it).
Output that starts &WARNING...& means that something probably
unintended happened due to the unexpected nature of your input or
Output that starts &DEBUG...& has (obviously enough) been
added to aid debugging.
Most of them should have been cleaned up
before release, but as Coot is constantly being developed, a few may
slip through.
Just ignore them.
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4 Coordinate-Related Features
4.1 Reading coordinates
The format
of coordinates that can be read by coot is either PDB or mmCIF.
coordinates, choose File -& Read Coordinates from the
Immediately after the coordinates have been read, the view is
(by default) recentred to the centre of this new molecule and the
molecule is displayed.
The recentring of the view after the coordinates
have been read can be turned off by unclicking the "Recentre?"
radio-button.
To disable the recentring of the view on reading a coordinates file via
scripting, use: (set-recentre-on-read-pdb 0).
However, when
reading a coordinates file from a script it is just as good (if not
better) to use (handle-read-draw-molecule-with-recentre
filename 0) - the additional 0 means &don't recentre&.
And that affects just the reading of filename and not
subsequent files.
Note that as of version 0.6.2 Coot can read MDL mol/mol2 files (the
atom names are not unique (of course), but at least you can see the
coordinates).
4.1.1 A Note on Space Groups Names
Coot uses the space group on the &CRYST1& line of the pdb file.
space group should be one of the xHM symbols listed (for example) in the
CCP4 dictionary file syminfo.lib.
So, for example, "R 3 2 :H"
should be used in preference to "H32".
4.1.2 Read multiple coordinate files
The reading multiple files using the GUI is not available (at the
However the following scripting functions are available:
(read-pdb-all)
which reads all the &*.pdb& files in the current directory
(multi-read-pdb glob-pattern dir)
which reads all the files matching glob-pattern in
directory dir.
Typical usage of this might be:
(multi-read-pdb "a*.pdb" ".")
Alternatively you can specify the files to be opened on the command
line when you start coot (see Section
4.1.3 SHELX .ins/.res files
SHELX ".res" (and ".ins" of course) files can be read into Coot, either
using the GUI File -& Open Coordinates... or by the
scripting function:
(read-shelx-ins-file file-name)
where file-name is quoted, such as "thox.ins".
Although Coot should be able to read any SHELX ".res" file, it may
currently have trouble displaying the bonds for centro-symmetric
structures.
ShelxL atoms with negative PART numbers are given alternative
configuration identifiers in lower case.
To write a SHELX ".ins" file:
(write-shelx-ins-file imol file-name)
where imol is the number of the molecule you wish to
This will be a rudimentary file if the coordinates were initially from a
"PDB" file, but will contain substantial SHELX commands if the
coordinates were initially generated from a SHELX ins file.
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4.2 Atom Info
Information about about a particular atom is displayed in the text
console when you click using middle-mouse.
Information for all the
atoms in a residue is available using Info -& Residue
The temperature factors
and occupancy of the atoms in a residue can be set by using
Edit -& Residue Info....
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4.3 Atom Labeling
Use Shift + left-mouse to label atom.
Do the same to toggle off the
The font size is changeable using Edit -&
Font Size....
The newly centred atom is labelled by default.
To turn this off use:
(set-label-on-recentre-flag 0)
Some people prefer to have atom labels that
are shorter, without the slashes and residue name:
(set-brief-atom-labels 1)
To change the atom label colour, use:
(set-font-colour 0.9 0.9 0.9)
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4.4 Atom Colouring
The atom colouring
system in coot is unsophisticated. Typically, atoms are coloured by
element: carbons are yellow, oxygens red, nitrogens blue, hydrogens
white and everything else green (see Section
for colour by chain).
However, it is useful to be able to distinguish
different molecules by colour, so by default coot rotates the colour
map of the atoms (i.e. changes the H value in the
colour system).
amount of the rotation depends on the molecule number and a
user-settable parameter:
(set-colour-map-rotation-on-read-pdb 30).
The default value is 31^\circ.
Also one is able to select only the Carbon atoms to change colour in
this manner: (set-colour-map-rotation-on-read-pdb-c-only-flag
The colour map rotation can be set individually for each molecule by
using the GUI: Edit -& Bond Colours....
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4.5 Bond Parameters
The various bond parameters can be set using the GUI dialog
Draw -& Bond Parameters or via scripting
functions.
The represention style of the molecule that has the active residue (if any)
can be changed using the scroll wheel with Ctrl and Shift.
4.5.1 Bond Thickness
The thickness (width) of
bonds of individual molecules can be changed.
This can be done via the
Bond Parameters dialog or the scripting interface:
(set-bond-thickness thickness imol)
where imol is the molecule number.
The default thickness is 3 pixels. The bond thickness also applies to
the symmetry atoms of the molecule. The default bond thickness for new
molecules can be set using:
(set-default-bond-thickness thick)
where thick is an integer.
There is no means to change the
bond thickness of a residue selection within a molecule.
4.5.2 Display Hydrogens
Initially, hydrogens are displayed.
They can be
undisplayed using
(set-draw-hydrogens mol-no 0)
where mol-no is the molecule number.
There is a GUI to control this too, under &Edit -& Bond Parameters&.
4.5.3 NCS Ghosts Coordinates
It is occasionally useful when analysing non-crystallographically
related molecules to have &images& of the other related molecules
appear matched onto the current coordinates.
It is important to
understand that these ghosts are for displaying differences of
NCS-related molecules by structure superposition, not displaying
neighbouring NCS related molecules.
As you read in coordinates in
Coot, they are checked for NCS relationships and clicking on &Edit -&
Bond Parameters -& Show NCS Ghosts& -& &Yes& -& &Apply& will
create &ghost& copies of them over the reference chain .
Sometimes SSM does not provide a good (or even useful) matrix.
case, we can specify the residue range ourselves and let the LSQ
algorithm provide the matrix.
A gui dialog for this operation can be
found under Extensions -& NCS -& NCS Ghosts by Residue
The scripting function is used like this:
(manual-ncs-ghosts imol resno-start resno-end ncs-chain-ids)
Typical usage: (manual-ncs-ghosts 0 1 10 (list "A" "B" "C"))
note that in ncs-chain-ids, the NCS master/reference
chain-id goes first.
4.5.4 NCS Maps
Coot can use the relative transformations of the NCS-related molecules
in a coordinates molecule to transform maps. Use Calculate
-& NCS Maps... to do this (note the NCS maps
only make sense in the region of the reference chain (see above).
Note also that the internal representation of the map is not
transformed.
If you try to export a NCS overlay map you will get an
untransformed map.
A transformed map only makes sense around a given
point (and when using transformed maps in Coot, this reference point is
changed on the fly, thus allowing map transformations on the fly).
[This applies to NCS overlap maps, NCS averaged maps are transformed].
This will also create an NCS averaged
4.5.5 Using Strict NCS
Coot can use a set of strict NCS matrices to specify NCS which means
that NCS-related molecules can appear like convention symmetry-related
molecules.
(add-strict-ncs-matrix imol ncs-chain-id ncs-target-chain-id m11 m12 m13 m21 m22 m23 m31 m32 m33 t1 t2 t3)
where ncs-chain-id might be "B", "C" "D" (etc.) and
ncs-target-chain-id is "A", i.e. the B, C, D molecules are
NCS copies of the A chain.
for icosahedral symmetry the translation components t1,
t2, t3 will be 0.
You need to turn on symmetry for molecule imol and set the
displayed symmetry object type to "Display Near Chains".
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4.6 Download coordinates
Coot provides the possibility to download coordinates from an
(e.g. EBI) server
-& Get PDB Using Code...). A pop-up entry box is
displayed into which you can type a PDB accession code.
then connect to the web server and transfer the file.
Coot blocks as
it does this (which is not ideal) but on a semi-decent internet
connection, it's not too bad.
The downloaded coordinates are saved
into a directory called coot-download.
It is also possible to download mmCIF data and generate a map.
currently requires a properly formatted database structure factors
mmCIF file .
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4.7 Get Coordinates and Map from EDS
Using this function we have the ability to download coordinates and view
the map from structures in the Electron Density Server (EDS) at Uppsala
University.
This is a much more robust and faster way to see maps from
deposited structures.
This function can be found under the File menu
This feature was added with the assistance of Gerard Kleywegt.
use the EDS, please cite GJ Kleywegt, MR Harris, JY Zou, TC Taylor, A
W&hlby & TA Jones (2004), "The Uppsala Electron-Density Server", Acta
Cryst. D60, .
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4.8 Save Coordinates
On selecting from the menus File -& Save
Coordinates... you are first presented with a list of molecules
which have coordinates.
As well as the molecule number, there is the
molecule name - very frequently the name of the file that was read in
to generate the coordinates in coot initially.
However, this is only
a molecule name and should not be confused with the filename to
which the coordinates are saved.
The coordinates filename can
be selected using the Select Filename... button.
If your filename ends in .cif, .mmcif or
.mmCIF then an mmCIF file will be written (not a &PDB&
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4.9 Setting the Space Group
If for some reason, the pdb file that you read does not have a space
group, or has the wrong space group, then you can set it using the
following function:
(set-space-group imol symbol)
(set-space-group 0 "P 41 21 2")
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4.10 Anisotropic Atoms
By default anisotropic atom information is
not represented .
To turn them on,
use Draw -& Anisotropic Atoms -& Show
Anisotropic Atoms?
-& Yes, or the command:
(set-show-aniso 1).
You cannot currently display thermal ellipsoids
isotropic atoms.
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4.11 Symmetry
Coordinates symmetry is &dynamic&.
Symmetry atoms
can be labeled .
Every time you recentre, the symmetry coordinates
are updated.
The information shown contains the atom information and
the symmetry operation number and translations needed to generate the
atom in that position.
By default symmetry atoms are not displayed.
If you want coot to display symmetry coordinates without having to use
the gui, add to your ~/.coot the following:
(set-show-symmetry-master 1)
The symmetry can be represented as C\alphas.
This along with representation of the molecule as
C\alphas (Section ) allow the production of
a packing diagram.
4.11.1 Missing symmetry
Sometimes (rarely) coot misses symmetry-related molecules that should be
displayed.
In that case you need to expand the shift search (the default is 1):
(set-symmetry-shift-search-size 2)
This is a hack, until the symmetry search algorithm is improved.
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4.12 Sequence View
The protein is represented by one letter codes
and coloured according to secondary structure.
These one letter codes
are active - if you click on them, they will change the centre of the
graphics window - in much the same way as clicking on a residue in the
Ramachandran plot.
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4.13 Print Sequence
The single letter code (of the imolth molecule) is written
out to the console in FASTA format.
Use can use this to cut and paste
into other applications:
(print-sequence imol)
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4.14 Environment Distances
Environment distances are turned on using Info -& Environment
Distances....
Contacts to other residues are shown and to
symmetry-related atoms if symmetry is being displayed.
The contacts
are coloured by atom type .
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4.15 Distances and Angles
The distance between atoms can be found using Info
-& Distance .
The result is displayed graphically, and written to the
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4.16 Zero Occupancy Marker
Atoms of zero occupancy are marked with a grey
spot. To turn off these markers, use:
(set-draw-zero-occ-markers 0)
Use an argument of 1 to turn them on.
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4.17 Atomic Dots
You can draw dots round arbitrary atom selections
(dots imol atom-selection dot-density radius)
The function returns a handle.
e.g. put a sphere of dots around all atoms of the 0th molecule
(it might be a set of heavy atom coordinates) at the default dot density
and radius:
(dots 0 "/1"
"heavy-atom-sites" 1 1)
You can't change the colour of the dots.
There is no internal mechanism to change the radius according to atom
With some cleverness you might be able to call this function
several times and change the radius according to the atom selection.
There is a function to clear up the dots for a particular molecule
imol and dots set identifier dots-handle
(clear-dots imol dots-handle)
There is a function to return how many dots sets there are for a
particular molecule imol:
(n-dots-set imol)
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4.18 Ball and Stick Representation
Fragments of the molecule can be rendered as a &ball and stick& molecule:
(make-ball-and-stick imol atom-selection bond-thickness sphere-size draw-spheres-flag)
(make-ball-and-stick 0 "/1/A/10-20" 0.3 0.4 1)
The ball-and-stick representation can be cleared using:
(clear-ball-and-stick imol)
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4.19 Mean, Median Temperature Factors
Coot can be used to calculate the
mean (average)
median temperatures factors:
(average-temperature-factor imol)
(median-temperature-factor imol)
-1 is returned if there was a problem .
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4.20 Secondary Structure Matching (SSM)
The excellent SSM alogrithm of Eugene Krissinel is available in Coot.
The GUI interface
is straight-forward and can be found under Calculate -& SSM
Superpose.
You can specify the specific chains that you wish to match
using the "Use Specific Chain" check-button.
There is a scripting level function which gives even finer control:
(superpose-with-atom-selection imol1 imol2
mmdb-atom-selection-string-1 mmdb-atom-selection-string-2
move-copy-flag )
the move-copy-flag should be 1 if you want to apply the
transformation to a copy of imol2 (rather than
imol2 itself). Otherwise, move-copy-flag
should be 0.
mmdb atom selection strings (Coordinate-IDs) are explained in detail in
the mmdb manual.
Briefly, the string should be formed in this manner:
/mdl/chn/seq(res).ic/atm[elm]:aloc
e.g. "/1/A/12-130/CA"
&p&&a href="http://www.ebi.ac.uk/~keb/cldoc/object/cl_obj_surf.html#CoordinateID"&The mmdb manual CoordinateID description&/a&.&/p&
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4.21 Least-Squares Fitting
There is a simple GUI for this Calculate -& LSQ Superpose...
The scripting interface to LSQ fitting is as follows:
(simple-lsq-match ref-start-resno ref-end-resno ref-chain-id imol-ref
mov-start-resno mov-end-resno mov-chain-id imol-mov
match-type)
ref-start-resno is the starting residue number
of the reference molecule
ref-end-resno is the last residue number
of the reference molecule
mov-start-resno is the starting residue number
of the moving molecule
mov-end-resno is the last residue number
of the moving molecule
match-type is one of 'CA,
'main, or 'all.
(simple-lsq-match 940 950 "A" 0 940 950 "A" 1 'main)
More sophisticated (match molecule number 1 chain &B& on to molecule
number 0 chain &A&):
(define match1 (list 840 850 "A" 440 450 "B" 'all))
(define match2 (list 940 950 "A" 540 550 "B" 'main))
(clear-lsq-matches)
(set-match-element match1)
(set-match-element match2)
(lsq-match 0 1) ; match molecule number 1 onto molecule number 0.
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4.22 Ligand Overlaying
The scripting function
(overlap-ligands imol-ligand imol-ref chain-id-ref resno-ref)
returns a rotation+translation operator which can be applied to other
molecules (and maps).
Here, imol-ligand is the molecule
number of the ligand (which is presumed to be a a molecule on its own -
Coot simply takes the first residue that it finds). imol-ref
chain-id-ref resno-ref collectively describe the target position for
the moving imol-ligand molecule.
The convenience function
(overlay-my-ligands imol-mov chain-id-mov resno-mov imol-ref chain-id-ref resno-ref)
wraps overlap-ligands.
The GUI for the function can be found under
Extensions -& Modelling -& Supperpose Ligands...
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4.23 Writing PDB files
As well as the GUI option File -& Save Coordinates... there
is a scripting options available:
(write-pdb-file imol pdb-file-name)
which writes the imolth coordinates molecule to
To write a specific residue range:
(write-residue-range-to-pdb-file imol chain-id start-resno
endresno pdb-file-name)
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5 Modelling and Building
The functions described in this chapter manipulate, extend or build
molecules and can be found under Calculate -&
Model/Fit/Refine....
When activated, the dialog "stays on top"
of the main graphics window .
Some people think that this is not always desirable, so
this behaviour can be undone using:
(set-model-fit-refine-dialog-stays-on-top 0)
5.1 Regularization and Real Space Refinement
Coot will read the geometry restraints for
refmac and use them in fragment (zone) idealization - this is called
&Regularization&.
The geometrical restraints
are, by default, bonds, angles, planes
and non-bonded
You can additionally use torsion restraints
by Calculate -& Model/Fit/Refine... -& Refine/Regularize Control
-& Use Torsion Restraints.
Truth to tell, this has not been
successful in my hands (sadly).
&RS (Real Space) Refinement&
(after Diamond,
1971 ) in Coot is the use of the map in addition to geometry terms to
improve the positions of the atoms.
Select &Regularize& from the
&Model/Fit/Refine& dialog and click on 2 atoms to define the zone
(you can of course click on the same atom twice if you only want to
regularize one residue).
Coot then regularizes the residue range.
the end Coot, displays the intermediate atoms in white and also
displays a dialog, in which you can accept or reject this
regularization.
In the console are displayed the \chi^2
values of the various geometrical restraints for the zone before
and after the regularization.
Usually the \chi^2 values are
considerably decreased - structure idealization such as this should
drive the \chi^2 values toward zero.
The use of &Refinement& is similar - with the addition of using a
The map used to refine the structure is set by using the
&Refine/Regularize Control& dialog.
If you have read/created only
one map into Coot, then that map will be used (there is no need to set
it explicitly).
Use, for example,
(set-matrix 20.0)
to change the weight of the map gradients to geometric gradients.
higher the number the more weight that is given to the map terms
default is 60.0.
This will be needed for maps generated from data not
on (or close to) the absolute scale or maps that have been scaled (for
example so that the sigma level has been scaled to 1.0).
For both &Regularize Zone& and &Refine Zone& one is able to use a
single click to
refine a residue range.
Pressing &A& on the keyboard while
selecting an atom in a residue will automatically create a residue
range with that residue in the middle.
By default the zone is
extended one residue either size of the central residue.
This can be
changed to 2 either side using (set-refine-auto-range-step
Intermediate (white) atoms can be moved around with the mouse (click
and drag with left-mouse, by default).
Refinement will proceed from the
new atom positions when the mouse button is released.
It is possible
to create incorrect atom nomenclature and/or chiral volumes in this
manner - so some care must be taken.
Press the &A& key as you
left-mouse click to move atoms more &locally& (rather than a linear
shear) and &Ctrl& key as you left-mouse click to move just one atom.
In more up to date versions, Coot will display colour patches (something
like a traffic light system)
representing the chi squared values of each
of types of geometric feature refined.
Typically &5 greens& is the
thing to aim for, the colour changes occurring at chi squared values 2, 5
and 8 (8 being the most red).
To prevent the unintentional refinement of a large number of residues,
there is a &heuristic fencepost& of 20 residues.
A selection of
than 20 residues will not be regularized or refined.
The limit can be
changed using the scripting function: e.g.
(set-refine-max-residues 30).
5.1.1 Dictionary
The geometry description for residues, monomers and links used by Coot
are in the standard mmCIF format.
Because this format alows multiple
comp_ids (residue types) to be described within a cif loop, it is hard
to tell when a dictionary entry needs to be overwritten when reading a
Therefore Coot makes this extra constraint: that the
&chem_comp& loop should appear first in the comp list data item - if
this is the case, then Coot can overwrite an old restraint table for a
particular comp_id/residue-type when a new one is read.
By default,
the geometry dictionary entries for only the standard
residues are read in at the start
It may be that your particular ligand is not amongst
To interactively add a dictionary entry use File
-& Import CIF Dictionary.
Alternatively, you can use
the function:
(read-cif-dictionary filename)
and add this to your .coot file (this may be the preferred
method if you want to read the file on more than one occasion).
Note: the dictionary also provides the description of the ligand's
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5.1.2 Sphere Refinement
Sphere refinement selects residues within a certain distance of the
residue at the centre of the screen and includes them for real space
refinement.
In this way, one can select residues that are not in a
linear range.
This technique is useful for refining disulfide bonds and
glycosidic linkages.
To enable sphere refinement, Right-mouse in the vertical toolbutton
menu, Manage buttons -& [Tick] Sphere Refine -& Apply.
You will need
a python-enabled Coot to do this.
The following adds a key binding (Shift-R) that refines resides that are
within 3.5&A of the residue at the centre of the screen:
(define *sphere-refine-radius* 3.5)
(add-key-binding "Refine residues in a sphere" "R"
(lambda ()
(using-active-atom
(let* ((rc-spec (list aa-chain-id aa-res-no aa-ins-code))
(ls (residues-near-residue aa-imol rc-spec *sphere-refine-radius*)))
(refine-residues aa-imol (cons rc-spec ls))))))
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5.1.3 Refining Specific Residues
You can specify the residues that you want to refine without using a
linear or sphere selection usine refine-residues.
For example:
(refine-residues 0 '(("L" 501 "") ("L" 503 "")))
will refine residues A501 and A503 (and residue A502 (if it exists)
will be an anchoring residue - used in optimizing the link geometry of
the atoms in A501 and A503).
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5.1.4 Refining Carbohydrates
Refining carbohydrates monomers should be as straightforward as refining
a protein residue.
Coot will look in the dictionary for the 3-letter
code for the particular residue type, if it does not find it, Coot will
try to search for dictionary files using &-b-D& or &-a-L& extensions.
When refining a group of carbohydrates, the situation needs a bit more
explanation. For each residue pair with tandem residue numbers specified
in the refinement range selection, Coot checks if these residue types
are are furanose or pyranose in the dictionary, and if the are both one
or the other, then it tries to see if there are any of the 11 link types
(BETA1-4, BETA2-3, ALPHA1-2 and so on) specified in the dictionary.
does this by a distance check of the potentially bonding atoms.
distance is less than 3.0&A, then a glycosidic bond is made and used
in the refinement.
Bonds between protein and carbohydrate and branched carbohydrates can be
refined using &Sphere Refinement&.
Instead of using a sphere to make a residue selection, you can specify
the residues directly using refine-residues, for example:
(refine-residues 0 '(("L" 501 "") ("L" 503 "")))
LINK and LINKR cards are not yet used to determine the geometry of the
restraints.
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5.1.5 Planar Peptide Restraints
By default, Coot uses a 5 atom (CA-1, C-1, O-1, N-2, CA-2) planar
peptide restraints.
These restraints should help in low resolution
fitting (the main-chains becomes less distorted), reduce accidental
cis-peptides and may help &clean up& Ramachandran plots.
(add-planar-peptide-restraints)
And similarly they can be removed:
(remove-planar-peptide-restraints)
There is also a GUI to add and remove these restraints in
Extensions -& Refine... -& Peptide Restraints...
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5.1.6 The UNK residue type
The UNK residue type is a special residue type to Coot.
been added for use with Buccaneer. Don't give you ligand (or anything
else) the 3-letter-code UNK or confusion will result
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5.1.7 Moving Zero Occupancy Atoms
By default, atoms with zero occupancy are moved when refining and
regularizing.
This can sometimes be inconvenient.
To turn of the
movement of atoms with zero occupancy when refining and regularizing:
(set-refinement-move-atoms-with-zero-occupancy 0)
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5.2 Changing the Map for Building/Refinement
You can change the map that is used for the fitting and refinement tools
using the Select Map... button on the Model/Fit/Refine
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5.3 Rotate/Translate Zone
&Rotate/Translate Zone& from the &Model/Fit/Refine& menu allows
manual movement of a zone.
After pressing the &Rotate/Translate Zone&
button, select two atoms in the graphics canvas to define a residue
range , the
second atom that you click will be the local rotation centre for the
The atoms selected in the moving fragment have the same
alternate conformation code as the first atom you click.
To actuate a
transformation, click and drag horizontally across the relevant button
in the newly-created &Rotation & Translation& dialog. The axis
system of the rotations and translations are the screen coordinates.
Alternatively
click using left-mouse on an atom in the fragment and drag the
fragment around. Use Control Left-mouse to move just one atom, rather
than the whole fragment.
If you click Control Left-mouse whilst not
over an atom then you can rotate the fragment using mouse drag.
Click &OK& (or press Return) when the transformation is complete.
To change the rotation point to the centre of the intermediate atoms
(rather than the second clicked atom), use the setting:
(set-rotate-translate-zone-rotates-about-zone-centre 1)
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5.4 Rigid Body Refinement
&Rigid Body Fit Zone& from the
&Model/Fit/Refine& dialog provides rigid body refinement.
selection is zone-based .
So to refine just one residue, click on one atom twice.
Sometimes no results are displayed after Rigid Body Fit Zone.
because the final model positions had too many final atom positions in
negative density.
If you want to over-rule the default fraction of
atoms in the zone that have an acceptable fit (0.75), to be (say)
(set-rigid-body-fit-acceptable-fit-fraction 0.25)
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5.5 Simplex Refinement
Rigid body refinement via Nelder-Mead Simplex minimization is available
Simplex refinement has a larger radius of convergence and thus
is useful in a position where simple rigid body refinement finds the
wrong minimum. However the Simplex algorithm is much slower.
refinement for a residue range start-resno to
end-resno (inclusive) in chain chain-id can
be accessed as follows:
(fit-residue-range-to-map-by-simplex start-resno end-resno alt-loc
chain-id imol imol-for-map)
There is currently no GUI interface to Simplex refinement.
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5.6 Post-manipulation-hook
If you wanted automatically run a function after a model has been
manipulated then you can do so using by creating a function that takes
2 arguments, such as:
(post-manipulation-hook imol manipulation-mode)
manipulation-mode is one of (DELETED),
(MUTATED) or (MOVINGATOMS).
And of course imol is the model number of the maniplated
(It would of course be far more useful if this function was also
passed a list of residues - that is something for the future).
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5.7 Baton Building
Baton build is most useful if a skeleton is already calculated and
displayed (see Section ).
When three or more atoms
have been built in a chain, Coot will use a prior probability
distribution for the next position based on the position of the previous
The analysis is similar to that of Oldfield & Hubbard (1994)
, however it is based on a
more recent and considerably larger database.
Little crosses are drawn representing directions in which is is
possible that the chain goes, and a baton is drawn from the current
point to one of these new positions.
If you don't like this
particular direction , use Try Another.
list of directions is scored according to the above criterion and
sorted so that the most likely is at the top of the list and displayed
first as the baton direction.
When starting baton building, be sure to be about 3.8&A from the
position of the first-placed C\alpha, this is because the next
C\alpha is placed at the end of the baton, the baton root being at
the centre of the screen.
So, when trying to baton-build a chain
starting at residue 1, centre the screen at about the position of
residue 2.
It seems like a good idea to increase the map sampling to 2 or even 2.5
(before reading in your mtz file) [a grid sampling of about 0.5&A
seems reasonable] when trying to baton-build a low resolution map.
can set the map sampling using Edit -& Map Parameters -& Map
Occasionally, every point is not where you want to
position the next atom.
In that case you can either shorten or
lengthen the baton, or position it yourself using the mouse.
&b& on the keyboard to swap to baton mode for the
Baton-built atoms are placed into a molecule called &Baton Atom& and
it is often sensible to save the coordinates of this molecule before
quitting coot.
If you try to trace a high resolution map (1.5&A
or better) you will
need to increase the skeleton search depth from the default (10), for
(set-max-skeleton-search-depth 20)
Alternatively, you could generate a new map using data
to a more moderate resolution (2&A), the map may be easier to
interpret at that resolution anyhow .
The guide positions are updated every time the &Accept& button is
The molecule name for these atoms is &Baton Build Guide Points&
and is is not usually necessary to keep them.
5.7.1 Undo
There is also an &Undo& button for baton-building.
Pressing this
will delete the most recently placed C\alpha and the guide points
will be recalculated for the previous position.
The number of
&Undo&s is unlimited.
Note that you should use the &Undo& button
in the Baton Build dialog, not the one in the &Model/Fit/Refine&
dialog (Section ).
5.7.2 Missing Skeleton
Sometimes (especially at loops) you can see
the direction in which the chain should go, but there is no skeleton
(see Section ) is displayed (and consequently no
guide points) in that direction. In that case, &Undo& the previous
atom and decrease the skeletonization level (Edit
-& Skeleton Parameters -& Skeletonization
Accept the atom (in the same place as last time) and now
when the new guide points are displayed, there should be an option to
build in a new direction.
5.7.3 Building Backwards
The following scenario is not uncommon: you find a nice stretch of
density and start baton building in it.
After a while you come to a
point where you stop (dismissing the baton build dialog).
You want to
go back to where you started and build the other way.
How do you do
Use the command:
(set-baton-build-params start-resno
chain-id "backwards")
where start-resno would typically
and chain-id would be
"" (default).
Recentre the graphics window on the first atom of the just-build
Select &Ca Baton Mode& and select a baton direction
that goes in the &opposite& direction to what is typically residue
This is slightly awkward because the initial baton atoms build
in the &opposite& direction are not dependent on the first few
atoms of the previously build fragment.
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5.8 Reversing Direction of Fragment
After you've build a fragment, sometimes you might want to change the
direction of that fragment (this function changes an already existing
fragment, as opposed to Backwards Building which sets up Baton Building
to place new points in reverse order).
The fragment is defined as a contiguous set of residues numbers.
that you should be sure that other partial fragments which have the same
chain id and that are not connected to this fragment have residue
numbers that are not contiguous with the fragment you are trying to
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5.9 C\alpha -& Mainchain
Mainchain can be generated using a set of C\alphas
as guide-points (such as those from Baton-building) along the line of
or Jones and
coworkers .
Briefly, 6-residue
fragments of are generated from a list of high-quality
structures. The C\alpha atoms of these fragments
are matched against overlapping sets of the guide-point C\alphas.
The resulting matches are merged to provide positions for the
mainchain (and C\beta) atoms.
This procedure works well for
helices and strands, but less well
for less common structural features.
This function is also available from the scripting interface:
(db-mainchain imol chain-id resno-start resno-end direction)
where direction is either "backwards" or "forwards".
Recall that the chain-id needs to be quoted, i.e.
use "A" not A.
Note that chain-id is
"" when the C\alphas have been built with Baton Mode in
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5.10 Backbone Torsion Angles
It is possible to edit the backbone \phi and \psi angles
indirectly using an option in the Model/Fit/Refine's dialog: &Edit
Backbone Torsions..&. When clicked and an atom of a peptide is
selected, this produces a new dialog that offers &Rotate Peptide&
which changes this residues \psi and &Rotate Carbonyl& which
changes \phi.
Click and drag across the button
the moving atoms in the graphics window.
You should know, of course,
that making these modifications alter the \phi/\psi angles of
more than one residue.
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5.11 Docking Sidechains
Docking sidechains means adding sidechains to a model or fragment that
has currently only poly-Ala, where the sequence assignment is unknown.
The algorithm is basically the same as in Cowtan's Buccaneer, but with
some corners cut to make things (more or less) interactive.
algorithm uses the shape of the density around the C-beta position to
estimate the probability of each sidechain type at that position.
The function is accessed via the Extensions -& Dock Sequence
menu item.
First, a sequence should be assigned from a PIR file to a
particular chain-id and model number.
Secondly Extensions -&
Dock Sequence -& Dock Sequence on this fragment....
Choose the
model to build on and then Dock Sequence! If all goes well,
the model will be updated with mutated residues and undergo rotamer
seach for each of the new residues.
If the sequence alignment is not
sufficiently clear, then you will get a dialog suggesting that you
extend or improve the fragment.
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5.12 Rotamers
The rotamers are generated
backbone independent sidechain library of the Richardsons group
The m, t and p stand for &minus (-60)&, &trans (180)& and &plus
There is one letter per \chi angle.
Use keyboard &.& and &,& to cycle round the rotamers.
5.12.1 Auto Fit Rotamer
&Auto Fit Rotamer& will try to fit the
rotamer to the electron density.
Each rotamer is generated, rigid
body refined and scored according to the fit to the map.
Fitting the
second conformation of a dual conformation in this way will often fail
- the algorithm will pick the best fit to the density - ignoring the
position of the other atoms.
The algorithm doesn't know if the other atoms in the structure are in
sensible positions.
If they are, then it is sensible not to put this
residue too close to them, if they are not then there should be no
restriction from the other atoms as to the position of this residue -
the default is &are sensible&, which means that the algorithm is
prevented from finding solutions that are too close to the atoms of
other residues. (set-rotamer-check-clashes 0) will stop this.
There is a scripting interface to auto-fitting rotamers:
(auto-fit-best-rotamer resno alt-loc ins-code chain-id
imol-coords
imol-