1. WINCOOT

2. What is COOT?
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Coot is for model building, model completion and
validation.
Coot displays maps and models and allows model
manipulations such as idealization, real space
refinement, manual rotation, rigid-body fitting,
ligand search, solvation, mutations, rotamers,
Ramachandran plots...
Coot is developed by Paul Emsley and Kevin
Cowtan from the university of York.

3. Versions of COOT…
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I have done my work on WinCoot 0.6 version
Now WinCoot 0.7.2 version is also available and it
is the latest one.
Almost all Coot functions are working.
There are also some bugs in this tool.

4. Functions of Coot…
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Symmetry
Electron density
Interface to REFMAC
Rigid-body refinement
Rotamers
Regularization and refinement
Finding ligands
Add terminal residue
Skeletonization and Ca building
Finding water molecules
I have focused on removing of outliers and rotamers.

5. Steps of Coot…
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I installed the Coot in my window XP.
Then I opened the tool Coot.
Here are some steps in which I have showed how to
remove outliers and rotamers.
For this I have already downloaded the 3D protein
structure from pdb, which I guess that it may have
some structural problems.

6. Go to file and click
on
Open coordinates to
open your protein
strctr.

7. Go to file of your
protein strctr. And
open it

8. Go to validate to
remove outliers

9. Go to
ramachandrn plot
and click on it to
remove outliers

10. 1)All the red dots
show
Outliers click on
one of them and
2) then click on ok
Note that
total
outliers are
30

11. 3) click on it

12. 4) click on selected
residue

13. 5) adjust peptide or carboxy
angles By moving them back
or forward until the selected
red outlier move in allow
region (pink or yellow) and
color shifted to blue
6) click ok

14. Again Go to
ramachandrn plot
and click on it

15. Note that now
total outliers
are 29
Repeat above
steps by
selecting
outliers one by
one and
shifting all
possible ones
to pink or
yellow region

16. To remove poor
rotamers click on it

17. A window like it will open
red bars shows poor
rotamers 1) click on one
of them 2) click on close

18. click on it

19. click on selected poor
rotamer

20. A window like it will open
3) click on ok without
making any chage

21. Again click on it

22. A window like it will open
red bar of poor rotamer is
removed
Repeat these steps of poor
rotamers until all the red
bars will removed

23. Validation…
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After this refinement again check your protein
structure through
•
mol-probity
NIH server
These are online tools from where we can validate
our refined structure.
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24. Aims of Coot…
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Easy to use
Powerful
Smooth interface to external applications

25. References…
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https://www.google.com.pk/url?sa=t&rct=j&q=&es
rc=s&source=web&cd=3&cad=rja&ved=0CDQQF
jAC&url=http%3A%2F%2Fwww.csb.yale.edu%2F
userguides%2Fgraphics%2Fcoot%2Fba5070.pdf&e
i=SYCfUvCqCOqt7QaJ64HgCg&usg=AFQjCNE
wyyupkQsFhPxrvsJOeoGSw3mI4Q&bvm=bv.571
55469,d.bGQ
http://www.ucl.ac.uk/~rmhasek/coot.html
http://en.wikipedia.org/wiki/Coot_(program)