<s>
The	O
program	O
Coot	B-Language
(	O
Crystallographic	O
Object-Oriented	O
Toolkit	O
)	O
is	O
used	O
to	O
display	O
and	O
manipulate	O
atomic	O
models	O
of	O
macromolecules	O
,	O
typically	O
of	O
proteins	O
or	O
nucleic	O
acids	O
,	O
using	O
3D	O
computer	O
graphics	O
.	O
</s>
<s>
Coot	B-Language
displays	O
electron	O
density	O
maps	O
and	O
atomic	O
models	O
and	O
allows	O
model	O
manipulations	O
such	O
as	O
idealization	O
,	O
real	O
space	O
refinement	O
,	O
manual	O
rotation/translation	O
,	O
rigid-body	O
fitting	O
,	O
ligand	O
search	O
,	O
solvation	O
,	O
mutations	O
,	O
rotamers	O
,	O
and	O
Ramachandran	B-Application
idealization	I-Application
.	O
</s>
<s>
Coot	B-Language
is	O
free	B-Application
software	I-Application
,	O
distributed	O
under	O
the	O
GNU	B-License
GPL	I-License
.	O
</s>
<s>
It	O
is	O
available	O
from	O
the	O
Coot	B-Language
web	O
site	O
originally	O
at	O
the	O
University	O
of	O
York	O
,	O
and	O
now	O
at	O
the	O
MRC	O
Laboratory	O
of	O
Molecular	O
Biology	O
.	O
</s>
<s>
Pre-compiled	O
binaries	O
are	O
also	O
available	O
for	O
Linux	B-Application
and	O
Windows	B-Application
from	O
the	O
web	O
page	O
and	O
CCP4	O
,	O
and	O
for	O
Mac	B-Operating_System
OS	I-Operating_System
X	I-Operating_System
through	O
Fink	B-Application
and	O
CCP4	O
.	O
</s>
<s>
Additional	O
support	O
is	O
available	O
through	O
the	O
Coot	B-Language
wiki	O
and	O
an	O
active	O
COOT	B-Language
mailing	O
list	O
.	O
</s>
<s>
Coot	B-Language
can	O
be	O
used	O
to	O
read	O
files	O
containing	O
3D	O
atomic	O
coordinate	O
models	O
of	O
macromolecular	O
structures	O
in	O
a	O
number	O
of	O
formats	O
,	O
including	O
pdb	O
,	O
mmcif	O
,	O
and	O
Shelx	O
files	O
.	O
</s>
<s>
Coot	B-Language
can	O
also	O
display	O
electron	O
density	O
,	O
which	O
is	O
the	O
result	O
of	O
structure	O
determination	O
experiments	O
such	O
as	O
X-ray	O
crystallography	O
and	O
EM	O
reconstruction	O
.	O
</s>
<s>
Electron	O
density	O
may	O
be	O
read	O
into	O
the	O
program	O
from	O
ccp4	O
or	O
cns	B-Application
map	O
formats	O
,	O
though	O
it	O
is	O
more	O
common	O
to	O
calculate	O
an	O
electron	O
density	O
map	O
directly	O
from	O
the	O
X-ray	O
diffraction	O
data	O
,	O
read	O
from	O
an	O
mtz	O
,	O
hkl	O
,	O
fcf	O
or	O
mmcif	O
file	O
.	O
</s>
<s>
Coot	B-Language
provides	O
extensive	O
features	O
for	O
model	O
building	O
and	O
refinement	O
(	O
i.e.	O
</s>
<s>
Coot	B-Language
provides	O
a	O
range	O
of	O
validation	O
tools	O
,	O
listed	O
below	O
.	O
</s>
<s>
Ramachandran	B-Application
plot	I-Application
-	O
validate	O
the	O
torsion	O
angles	O
of	O
a	O
protein	O
chain	O
.	O
</s>
<s>
Coot	B-Language
is	O
built	O
upon	O
a	O
number	O
of	O
libraries	O
.	O
</s>
<s>
Other	O
dependencies	O
include	O
FFTW	B-Application
,	O
and	O
the	O
GNU	B-Application
Scientific	I-Application
Library	I-Application
.	O
</s>
<s>
The	O
CCP4mg	O
molecular	O
graphics	O
software	O
from	O
Collaborative	O
Computational	O
Project	O
Number	O
4	O
is	O
a	O
related	O
project	O
with	O
which	O
Coot	B-Language
shares	O
some	O
code	O
.	O
</s>
<s>
The	O
projects	O
are	O
focused	O
on	O
slightly	O
different	O
problems	O
,	O
with	O
CCP4mg	O
dealing	O
with	O
presentation	O
graphics	O
and	O
movies	O
,	O
whereas	O
Coot	B-Language
deals	O
with	O
model	O
building	O
and	O
validation	O
.	O
</s>
