WINCOOT

What is COOT?

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.

Versions of COOT…

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.

Functions of Coot…

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.

Steps of Coot…

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.

Go to file and click on

Open coordinates to open your protein strctr.

Go to file of your protein strctr. And

open it

Go to validate to remove

outliers

Go to ramachandrn plot and click

on it to remove outliers

1)All the red dots show

Outliers click on one of them

and 2) then click on ok

Note that total

outliers are 30

3) click on it

4) click on selected residue

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

Again Go to ramachandrn plot and click

on it

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

To remove poor rotamers click on

it

A window like it will open red bars shows

poor rotamers 1) click on one of them 2)

click on close

click on it

click on selected poor rotamer

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

chage

Again click on it

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

Validation…

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.

Aims of Coot…

Easy to use Powerful Smooth interface to external applications

References…

https://www.google.com.pk/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&cad=rja&ved=0CDQQFjAC&url=http%3A%2F%2Fwww.csb.yale.edu%2Fuserguides%2Fgraphics%2Fcoot%2Fba5070.pdf&ei=SYCfUvCqCOqt7QaJ64HgCg&usg=AFQjCNEwyyupkQsFhPxrvsJOeoGSw3mI4Q&bvm=bv.57155469,d.bGQ

http://www.ucl.ac.uk/~rmhasek/coot.html http://en.wikipedia.org/wiki/Coot_(program)