Coot

angel may

Is this the “Official Home of Coot on the Web™”? Yes – welcome. What does Coot stand for? Crystallographic Object-Oriented Toolkit What does it do? Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. Coot displays maps and models and allows […]


Is this the “Official Home of Coot on the Web™”?

Yes – welcome.


What does Coot stand for?

Crystallographic Object-Oriented Toolkit

What does it do?

Coot is for macromolecular model building, model completion
and validation, particularly suitable for protein modelling using
X-ray data.

Coot displays maps and models and allows model manipulations
such as idealization, real space refinement, manual
rotation/translation, rigid-body fitting, ligand search,
solvation, mutations, rotamers, Ramachandran plots, skeletonization,
non-crystallographic symmetry and more.





What’s the latest stable release?

0.9

Where are the release binaries?

Coming soon…

What’s it like?

Coot has some features that resemble those of Frodo, O, Quanta
and XtalView’s XFit. It is a completely independent system of
course. Coot doesn’t do many aspects of structure represention
(for example ribbons or sophisticated colouring schemes).

Coot is under development. New features are being added. There
may be bugs (although I do put some effort into cutting down the bug count).

Is there a Coot FAQ?

Yes.

Is there a Coot Mailing list?

There is a Coot email list now hosted by the jiscmail service :

http://www.jiscmail.ac.uk/lists/coot.html




Is there Coot documentation?

Yes….

The 2012 ACA Coot Basics can be found here.

The 2012 ACA Coot Extras can be found here.

The 2010 CCP4 Study weekend presentation can be found here.

How do I cite Coot?

Please see the FAQ. Get the paper.

I like to spell Coot with a capital “C” and
lower-case “oot”, with italics. I am not dogmatic about
it.

OK, how does it look?

Like this:


snapshot

How this picture was made

Hmm… very pretty. Any other piccies?

Try here.

What formats?

PDB, mmCIF, MTZ files, .phs and others.

It makes maps from MTZ and .phs files?

Yep.

Can it read conventional CCP4 maps?

Yep.

Can it read any other kind of map?

Yes, it can read CNS maps.

Is it scriptable?

Yep, hundreds of functions are made
available to the user via SWIG
and can be scripted in either Python or scheme.

Where do I get it?

See the sidebar.

Which binary should I use? See the FAQ.

How do I install it?

Read the README in the source tar
file.

What libraries do I need?

  • fftw
  • mmdb
  • ccp4c
  • clipper
  • guile or Python
  • glib
  • GTK+-2 and gdk
  • pthread
  • gtkglext
  • gnome-canvas
  • zlib
  • GSL
  • GL
  • GLU
  • glut

Errg. Sounds complicated.

Yes, it is a bit.
Binary distributions for a selection of systems are built
every night.

There is an “autobuilder”
build script
which we use to make build the binaries.

I should add that Coot depends on many other projects, some
general (GTK+, the GNU Scientific Library, python, guile, GL
graphics libraries and toolkits) and others more specific to
structural biology (mmdb, clipper) which are fundamental to the
design and implementation of the program.

What is the licence?

Mostly GPLv3, some GLPv2+, some LGPLv3.

So I can just download it and use it, no questions asked?

Yep. Be my guest.

Even if I’m part of a Big Pharma?

Yes.

On which platforms does it run?

Certainly on Ubuntu, Fedora, RedHat Enterprise Linux, Microsoft Windows, MacOS X.
You can get WinCoot here.

Getting the Coot binaries to run on RHEL, or SuSe might take a bit more
effort. Please see the Coot FAQ.


Will you ever release version 1.0?

Yes, there is a road-map to 1.0. ETA 18 months.

Isn’t that what you said 18 months ago?

Yes. Things happened. Important things. But not Coot releases.

Not to be confused with:

Alwyn Jones’ O,
Quanta,
XtalView,
CCP4mg.

What is the Coot holding in its beak, by the way?

It’s biting off the gamma phosphate of an ATP.

And that’s supposed to be an allusion to a biochemical process, is it?

Err.. yes.

Most likely to say:

“Now how does that Refmac button work again..?”

Least likely to say:

“On reflection, it’d have been much better to implement using Tcl/Tk.”


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