--- The Detailed Node Listing ---
Building and Installing
Which binary tar file shall I use?
Configuration Problems
Using Coot
Other Coot Information
The reference for Coot has been published: You can use this BibTeX database entry (which can be imported into EndNote)... format as you please:
@Article{emsley2010:coot,
author = {Paul Emsley and Bernhard Lohkamp and William G. Scott and Kevin Cowtan},
title = {Features and Development of Coot},
journal = {Acta Crystallographica Section D - Biological Crystallography},
year = 2010,
volume = 66,
pages = 486-501
}
The Coot paper has published in the proceedings of the 2009 CCP4 Study Weekend.
You can download the 2010 paper here:
For the sake of completeness, you can download the old 2004 paper here:
See Bill Scott's Coot Page:
Download the appropriate tar file for you system. Untar it. Add the bin directory (the one that contains coot and coot-real) to your path and you are ready to go... You should not need to edit or use the setup/coot* files.
Download the appropriate tar file for you system. Untar it. Add the bin directory (the one that contains coot and coot-real) to your path and you are ready to go... You should not need to edit or use the setup/coot* files
Nancy Vogelaar used the RedHat 8 binary distribution and needed to do some extra fiddling - documented here:
Raji Edayathumangalam used the RedHat 7.2 binary distribution on Mandrake Linux 8.2 and needed to do some extra fiddling, documented here:
http://www.ysbl.york.ac.uk/%7Eemsley/coot/raji-mandrake.txt
Coot runs on Fedora Core 4, using the Fedora Core 3 binaries after making the following link:
| $ ln -s /usr/lib/libpt_linux_x86_r.so.1.8.4 $COOT_PREFIX/lib/libpt.so.1.6.5 |
Kay Diederichs reports that coot-0.0.18-binary-Linux-Fedora-Core-1.tar.gz works with RedHat Enterprise 3 if one makes the following link first:
| $ ln -s /usr/lib/libpt.so.1.4.7 $COOT_PREFIX/lib/libpt.so.1.5.0 |
Dirk Kostrewa thought that it was not necessary to make this link using the current Red Hat 8 binary tar.
Robert Dagil found that if he used the Coot binary-Linux-x86_64-centos-5-python-gtk2, then he could get Coot to start if he added the following links to in the lib directory of the coot binary distro.
|
ln -s libldap-2.2.so.7 -> /usr/lib64/libldap-2.4.so.2
ln -s libssl.so.4 -> /usr/lib64/libssl.so.1.0.0 ln -s libcrypto.so.4 -> /usr/lib64/libcrypto.so.1.0.0 |
Michael Latchem reports that coot-0.0.20-binary-Linux-Fedora-Core-1.tar.gz works with SuSE 9.1 if one makes the following link first:
| $ ln -s /usr/lib/libpt_linux_x86_r.so.1.6.5 $COOT_PREFIX/lib/libpt.so.1.5.0 |
Christophe Briand reports that Coot version 0.1 runs on Suse 9.3, using the Redhat 8 binary after making the following link
| $ ln -s /usr/lib/libImlib2.so.1.1.1 /usr/lib/libImlib.so.11 |
I presume that this would also work:
| $ ln -s /usr/lib/libImlib2.so.1.1.1 $COOT_PREFIX/lib/libImlib.so.11 |
You need to install the imlib-1.9.14-215 rpm
| ln -s /opt/gnome/lib64/libImlib.so.1.9.14 $COOT_PREFIX/lib/libImlib.so.11 |
or (depending on your architecture):
| ln -s /opt/gnome/lib/libImlib.so.1.9.14 $COOT_PREFIX/lib/libImlib.so.11 |
Dirk Kostrewa has got coot working on his Debian system. Here are his notes:
You will need (if you don't alread have them) fw_gcc fw_urt fw_libungif (i.e. libungif) and imlib from
http://freeware.sgi.com/fw-6.2/index-by-alpha.html
The md5sum is a means to determine if the file was corrupted during transfer. Run md5sum on the downloaded tar file and compare the result to the md5sum file on the server. If the results are the same, then the tar file is uncorrupted (or more strictly speaking: is corrupted in the same way as the file on the server).
$ coot coot: error while loading shared libraries: libpt.so.1.6.5: cannot open shared object file: No such file or directory
You need to install pwlib:
pwlib-1.6.5-1
$ coot dyld: coot version mismatch for library: /sw/lib/libtiff.3.dylib (compatibility version of user: 3.6.0 greater than library's version: 3.5.0)
This is because you have the default fink (stable). Coot is part of unstable fink so you need to enable the unstable branch (see Bill Scott's page (above)).
dyld: Symbol not found: __cg_jpeg_resync_to_restart Referenced from: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/ImageIO Expected in: /Users/xxx/coot-0.1.2_bin/lib/libjpeg.62.dylib
Atsushi Nakagawa says that this can be fixed by replacing xxx/Darwin-chihiro.chem.york.ac.uk-pre-release/lib/libjpeg.dylib with /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib
Or read the advice in $COOT_PREFIX/bin/coot about Intel Mac usage.
./coot: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory
You need to install these rpms:
freeglut-2.2.0-14 freeglut-devel-2.2.0-14
I don't know why it crashes. To work around, comment out (with a semicolon) "hello.scm" in the $COOT_PREFIX/share/coot/scheme/coot.scm file.
It's somewhat involved, but hopefully straightforward if you follow the autobuilder:
http://coot.googlecode.com/svn/trunk/build-it-gtk2-simple
Coot requires mmdb, clipper, glut, gtk, gtkglext. gtkglext requires GTK and OpenGL. gtk requires glib. clipper requires fftw, mccp4 and mmdb. Optionally you can enhance coot using gtk-canvas, libSSM, guile/guile-gtk/guile-gui/guile-www or python (the support for python is not so advanced).
These issues are sorted out in the autobuilder. Just download it, change a few parameters to fit your personal system at the top and execute it.
For general background on what a software developer wants to see (and not see) in a bug report:
http://www.chiark.greenend.org.uk/~sgtatham/bugs.html
For the case of Coot, I would also like to know the exact binary you are using
coot --version-full
and the operating system that you are running it on.
Also, the last several lines of the console output is often useful.
$ coot Acquiring application resources from /usr/programs/COOT/Linux-utonium.chem.york.ac.uk/share/coot/cootrc INFO:: splash_screen_pixmap_dir /usr/programs/COOT/Linux-utonium.chem.york.ac.uk/share/coot/pixmaps [snip] initializing molecules...done ERROR: In procedure primitive-load-path: ERROR: Unable to find file "ice-9/boot-9.scm" in load path
You need to install guile. We have the following guile packages:
umb-scheme-3.2-32 guile-devel-1.6.4-11 guile-1.6.4-11
You mean this one?
load "coot-gui.scm" (Error in proc: misc-error args: (#f ~A ~S (no code for module (gtk gdk)) #f))
You need to install guile-gtk. Here is the source, but your distribution may have rpms or debs.
http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/guile-gtk/guile-gtk-0.41.tar.gz
Martin Moncrieffe found a way:
http://www.biop.ox.ac.uk/coot/doc/martin-moncrieffe.txt
You mean something like this?
http://www.biop.ox.ac.uk/coot/doc/ugly.png
You have a non-default language. setenv LANG C (or LANG=C if you prefer) before starting coot. This has recently been added to the setup files in the source code (it is not in version 0.0).
The problem may also be due to LC_ALL. So, if the above doesn't work try also:
$ setenv LC_ALL C
Edit /Library/Coot/etc/gtk-2.0/gtkrc and set
gtk-font-name = "Sans 9"
Like this:
http://www.ysbl.york.ac.uk/%7Eemsley/coot/coot-startup.log
Things to look out for: Error reading all scm files, error reading Refmac dictionary files, error reading colours.def, error reading syminfo.lib, error finding splash-screen image, error reading cootrc file, error finding reference structures (e.g. from COOT_REF_STUCTS). So, if you get error messages or warning when coot start, you can expect it to be other than fully functional.
e.g.
Gtk-WARNING **: Unable to locate loadable module in module_path: "libbluecurve.so"
No, don't worry - Gtk just can't find a theme. Things will look a bit different to how they otherwise might, but everything will still work.
These messages:
Some deprecated features have been used. Set the environment variable GUILE_WARN_DEPRECATED to "detailed" and rerun the program to get more information. Set it to "no" to suppress this message. ObjectCache: Leaked 0002 refs to P 2ac 2ab ObjectCache: Leaked 0002 refs to P 2ac 2ab Nuvw = ( 108, 132, 64)} are nothing to worry about. I will clean them up one day (for release 0.7, I hope).
The default window focusing (using Metacity I believe) is a PITA when using Coot. Try this:
Hat -> Preferences -> Windows -> Select windows when the mouse moves
over them: check that box.
Hat --> Preferences -> Windows -> To move a window, press and hold
this key then grab the window:
Change from
Control
to Alt or Super
The default window focusing with the Aqua window manager is a PITA when using Coot. Try typing in a terminal this to set "Focus Follows Mouse":
$ defaults write com.apple.x11 wm_ffm true
On a more modern version of Mac OS X (10.5+), that might be:
$ defaults write org.x.X11 wm_ffm true
(thanks to William Scott for pointing that out).
You might need to restart X11 to activate this setting.
You can use this setting:
X11 -> Preferences -> Emulate 3 Button mouse
It will simulate the pressing of middle and right mouse when you use it in conjunction with Option and Apple keys.
Keyboard + and -.
One problem could be that the symmetry and cell of the map does not match the symmetry and cell of the related protein.
Or perhaps it's because Coot does not use the "viewing" contour level to generate blob map point clusters, i.e. it could be using a contour level much below what you are looking at. Coot positions the view at the centre of a blob. If the blob consists of an "arc" of points (as is often the case) the centre of the blob will not be in the blob.
"Add Terminal Residue" is known to be slow on sgi machines (hours, perhaps even a day). I don't know why.
"I can't see the contour level at the top of the screen or and the atom labels are faint or non-existant."
This seems like a graphics driver bug, or a hardware problem. If you turn the screenbackground white you might be able to see the text.
If you bring the atom to the centre of the screen, the atom label becomes more readable.
Edit -> Preferences -> Smooth Recentering -> Number of Steps -> 10
"I'm bored of moving the dialogs around every coot session. How do I make coot know where I want them?
You can use the "Position Dialogs" function in the Extensions ->
Settings menu.
For a more manual way, try
http://www.ysbl.york.ac.uk/%7Eemsley/coot/position-dialogs.txt.
It works in quad buffered stereo mode ("stereo-in-a-window"). You will
need a recent version and either use the Draw -> Stereo dialog
or pass the argument --stereo.
Yes.
Yes. Remember to use the DVI cable (not VGA) [thanks Allen Sickmier].
Warren DeLano: A line width of 2 pixels wide or greater is essential for achieving a good stereo effort with electron density meshes, "wire" bonds, etc.
You can achieve this in Coot using:
(set-map-line-width 2)
You might like also to turn on antialiasing (see below).
The build-in antialiasing in Coot is not very good - it needs to be improved.
If you have an nvidia card, you can turn on antialiasing using the environment variable __GL_FSAA_MODE. I set it to 5 for my graphics card, the best setting (in the range 1-20 or so) depends on your hardware.
Alternatively, use nvidia-settings
Antialiasing Settings -> Override Application Setting, 16x Antialiasing (on the slider)
Then restart coot.
[You will need to set up your screen for quad-buffered stereo system (not the more usual "full-screen" stereo) to even begin thinking about it].
Sue Roberts has some useful advice
http://www.ysbl.york.ac.uk/%7Eemsley/coot/s-roberts.txt.
So does Dirk Kostrewa:
http://www.ysbl.york.ac.uk/%7Eemsley/coot/dirk-k-irix-stero.txt.
Kevin Cowtan:: Change the setting in CNS which controls the extent of the output map. Instead of outputting a map covering a single molecule, you need to output a map covering a whole asymmetric unit (or if you prefer a whole unit cell).The X-PLOR maps output by CNS are output in O mode, not Coot mode, by default. This is due to a fundamental difference in understanding what a map is between programs which work crystal space (e.g. Coot, Quanta, XtalView) and those which don't.
Green is positive
Red is negative
To change the colour scheme (other than simply changing the map colour wheel):
(set-swap-difference-map-colours 1)
There are 2 ways. Either create a file called refmac-extra params in the directory in which you started coot, e.g. "http://www.ysbl.york.ac.uk/%7Eemsley/coot/refmac-extra-params"
or
define (for example in you $HOME/.coot file) the variable
refmac-extra-params, e.g.
(define refmac-extra-params
(list "WEIGHT 0.1"
"SOLVENT NO"
"REFI BREF ISOT"
"NCYCLES 6"))
(You can then use Measures -> Pointer Distances if you wish.)
Cntl Left-mouse-click over an intermediate (white) atom. Drag and drop. Make sure that you have focus in the graphics window when you press Ctrl (which, in Windows, that the graphics window has a blue title bar rather than a grey one). (You need to means be precise with the clicking - if the view rotates instead of the atom moving then you know that you have been insufficiently precise.)
The best way to fix that is to add proper (bonding) restraints between the metal and the sidechain (type).
If those are not available, you can mask out the density of the metals.
Extensions -> Maps -> Mask Map by Atom Selection...
For example, atom selection of "//B/[CO]" will remove all the
density for Cobalts in the "B" chain.
Then you will need to set the masked map as the map to be used for refinement, of course.
The bar heights are set to be sensible for average resolution data on the absolute scale. If that is not the case for your data then you may well see red bars.
You can change the scale:
Extensions -> Refine... -> Set Density Fit Graph Weight...
Like this:
;; Bind a function to the "v" key (Shift-V would be bound to "V").
(add-key-binding "Place atom at pointer" "v"
(lambda ()
(set-pointer-atom-is-dummy 1)
(place-atom-at-pointer)))
By default, Coot cleans out the coot-backup directory files older than 7 days every 7 days. If you want Coot to clean up all backup files every time it exits, add this to your ~/.coot file.
(define clear-backups-maybe (lambda () (delete-coot-backup-files
'delete) #f))
Question:: I have a residue that has one or more missing mainchain atoms. I want to mutate a "fresh" residue in - but I can't. What should I do?
Answer: If any of the CA, C or N atoms of a residue are missing then mutate can't work (it needs these atoms to do the least-squares fit). This is what I do in such a case: first delete the residue, then add a new one with "Add Terminal Residue..." then "Mutate -> Auto Fit..." to the required type, then Refine Zone.
Coot is built on many different OS types, using the given (or supplied) version of GTK+. Some old operating systems have a version of GTK+ that does not include a “ToolMenuButton” (newer operating systems do, of course) - and the toolbar menu Rotate/Translate function has uses such a widget. The Coot build sytem detects old versions of GTK+ and skips over the ToolMenuButton code, so the button does not appear in the main window. However, on all systems, the Rotate/Translate mode selector can be found as a menu to the right of the “Rotate/Translate Zone” button on the Model/Fit/Refine dialog.
So, if you want a Rotate/Translate Tool Menu Button in the main window, don't use an old OS (or more accurately, don't use a Coot binary built for an old OS).
You can also remove it by hand: edit xxx/share/coot/scheme/coot-gui.scm and comment out (with a ";") the "(old-coot?)" line.
You can also remove the old coot warning by running this script:
http://www.biop.ox.ac.uk/coot/extras/remove-old-coot-warning.sh
Yes, Extensions -> Settings -> Set Spin Speed.
No.
Yes.
$ coot –pdb pdb-1.pdb –pdb pdb-2.pdb –pdb pdb-3.pdb etc.
For tcsh, add this to you $HOME/.tcshrc (or $HOME/.cshrc file, if that's what you use):
set noglob
complete coot \
n/--coords/f:*{.pdb,.res,.brk,.brk.gz,.ent,.ent.gz,.pdb.gz}/ \
n/--data/f:*{.mtz,.cif,.fcf}/ \
n/--auto/f:*.mtz/ \
n/--script/f:*{.scm,.py}/ \
c/--/"(data auto coords script small no-graphics no-state-script)"/
unset noglob
The issue here is the backup directory coot-backup. By default, it
is created with strict permissions. I would recommend creating a
directory to which you both can write and setenv
COOT_BACKUP_DIR to that directory.
Extensions -> Modelling -> Residues with CIS Peptide Bonds
There are a number of solutions, depending on the problem
The command is:
(superpose-with-atom-selection imol-1 imol-2 atom-selection-string-1 atom-selection-string-2 move-copy-flag)
where:
imol-1 is the molecule number of the reference atoms
imol-2 is the molecule number of the molecule to be moved
the selection strings are mmdb atom selection string
the move-copy-flag is either 1 or 0 signalling if a copy of the imol-2 molecule should be moved (or the imol-2 molecule itself).
Typical usage might be:
(superpose-with-atom-selection 0 1 "//A/20-80" "//B/30-90" 1)
You can add any number of LSQ matches using
(add-lsq-match resno-start-ref resno-end-ref
chain-id-ref
resno-start-moving resno-end-moving
chain-id-moving
match-type
)
where
match-type is 0 for all-atom, 1 for mainchain and 2 for CAs.
For example:
(clear-lsq-matches)
(add-lsq-match 120 180 "A" 130 190 "B" 2)
(add-lsq-match 220 280 "A" 230 290 "B" 2)
(apply-lsq-matches)
Ligand superposition is performed using a graph-based match - i.e. there is no need to have matching atom names.
(overlap-ligands imol-ligand imol-ref chain-id-ref resno-ref)
this presumes that there is only the ligand in the imol-ligand molecule.
Typical usage:
(overlap-ligands 2 1 "A" 50)
Bernhard Lohkamp has a web page for WinCoot http://www.chem.gla.ac.uk/%7Ebernhard/coot/wincoot.html and a FAQ http://www.chem.gla.ac.uk/%7Ebernhard/coot/wincoot-faq.html
You can find links to WinCoot (and other) pre-release binaries here: http://www.biop.ox.ac.uk/coot/devel/build-info.html.
Coot uses clipper's Ramachadran data - which is the Richardson's Top500: http://kinemage.biochem.duke.edu/databases/top500.php
The Richardsons' (Son of Penultimate) Rotamer Library.
By using google. For example, if you wanted to make a search for Coot's "virtual trackball", use the google search:
virtual trackball coot site:www.biop.ox.ac.uk