Coot Tutorial

CCP4 School APS 2009 January 21, 2010

Contents
1 2 Mousing Introductory Tutorial 2.1 Get the les . . . . . . . . . 2.2 Start Coot . . . . . . . . . . . 2.3 Display Coordinates . . . . 2.4 Adjust Virtual Trackball . . 2.5 Display maps . . . . . . . . 2.6 Zoom in and out . . . . . . . 2.7 Recentre on Different Atoms 2.8 Change the Clipping (Slab) 2.9 Recontour the Map . . . . . 2.10 Change the Map Colour . . 2.11 Select a Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 2 2 2 2 3 4 4 6 8 8 8 8

Model Building 9 3.1 Rotamers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 3.2 More Real Space Renement . . . . . . . . . . . . . . . . . . . . . . . . 10 Blobology 4.1 Find Blobs . . 4.1.1 Blob 3 4.1.2 Blob 2 4.1.3 Blob 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 11 11 12 12 13 13 14 15 16 16 17

Extra Fun (if you have time) 5.1 Waters . . . . . . . . . . . . . . . . . 5.2 Working with NCS . . . . . . . . . . 5.3 Add Terminal Residue . . . . . . . . 5.4 Display Symmetry Atoms . . . . . . 5.5 Skeletonization and Baton Building . 5.6 Rene with Refmac . . . . . . . . . .

Use the EDS 17 6.1 Make a (Pretty?) Picture . . . . . . . . . . . . . . . . . . . . . . . . . . 17

1 Mousing
First, how do we move around and select things? Left-mouse Drag Ctrl Left-Mouse Drag Shift Left-Mouse Right-Mouse Drag Middle-mouse Scroll-wheel Forward Scroll-wheel Backward Rotate view Translates view Label Atom Zoom in and out Centre on atom Increase map contour level Decrease map contour level

2 Introductory Tutorial
In this tutorial, we will learn how to do the following: 1. Start Coot 2. Display coordinates 3. Display a map 4. Zoom in and out 5. Recentre on Different Atoms 6. Change the Clipping (Slab) 7. Recontour the Map 8. Change the Map Colour 9. Display rotamers and rene residue

2.1 Get the les

Before we start, lets get the les on which we will be working:
$ wget http://www.ysbl.york.ac.uk/emsley/coot/tutorial/tutorial-modern.pdb $ wget http://www.ysbl.york.ac.uk/emsley/coot/tutorial/rnasa-1.8-all refmac1.mtz

or copy them from /home/emsley/tutorial

2.2 Start Coot

To use coot, in a terminal window, type: $ coot When you rst start coot, it should look something like Figure 1.

2.3 Display Coordinates

So lets read in those coordinates: Select File from the Coot menu-bar1
1 Note

you can also use Alt-F instead of clicking on File

Figure 1: Coot at Startup Not much to see at present... Actually, after this, coot screenshots will be displayed with a white background, whereas you will see a black one

Select the Open Coordinates menu item

[Coot displays a Coordinates File Selection window]

Either Select tutorial-modern.pdb from the Files list or Type tutorial-modern.pdb in the Selection: entry Click OK in the Coordinates File Selection window

[Coot displays the coordinates in the Graphics Window]

2.4 Adjust Virtual Trackball

By default, Coot has a virtual trackball to relate the motion of the molecule to the motion of the mouse. Many people dont like this. So you might like to try the following. In the Coot main menu-bar: Edit Preferences. . . [Coot displays a Preferences window] On the left toolbar select General and then on the right top notebook tab HID. Select Flat to change the mouse motion. (Use the Spherical Surface option to turn it back to how it is by default). What is the difference? Flat mode is like the mode used by O. In both modes, dragging the mouse near the centre of the screen causes the view to rotate about the X- or Y- axis. However in spherical mode you can also rotate about the z-axis by dragging the mouse along an edge of the window.

Figure 2: Coot After Loading Coordinates

2.5 Display maps

We are at the stage where we are looking at the results of the renement. The renement programs stores its data (labelled lists of structure factor amplitudes and phases) in an MTZ le. Lets take a look. . . Select File from the Coot menu-bar Select Auto Open MTZ menu item [Coot displays a Dataset File Selection window] Select the lename rnasa-1.8-all refmac1.mtz If you choose instead Open MTZ, cif or phs... you will see: [Coot displays a Dataset File Selection window] Select the lename rnasa-1.8-all refmac1.mtz

[Coot displays a Dataset Column Label Selection window]

Notice that you have a selection of different column labels for the Amplitudes and Phases, however, lets use the defaults: FWT and PHWT. Press OK in the Column Label Window Now open the MTZ le and select column labels DELFWT and PHDELWT. So now we have 2 maps (whether auto-opened or not).

2.6 Zoom in and out

To zoom in, click Right-mouse and drag it left-to-right2 . To zoom out again, move the mouse the opposite way.
2 or

up-to-down, if you prefer that

Figure 3: Coot MTZ Column Label Selection Window

Figure 4: Coot after reading an MTZ le and zoomed in.

2.7 Recentre on Different Atoms

Select Draw from the Coot menu-bar Select Go To Atom. . .

[Coot displays the Go To Atom window]

Expand the tree for the A chain Select 1 ASP in the residue list Click Apply in the Go To Atom window At your leisure, use Next Residue and Previous Residue (or Space and Shift Spacein the graphics window) to move along the chain. Click Middle-mouse over an atom in the graphics window

[Coot recentres on that atom]

Ctrl Left-mouse & Drag moves the view around. If this is a too slow and jerky: Select Edit Preferences. . . from Coots menu-bar Select the Maps toolbutton on the left Select the Dragged Map notebook tab. Select No in the Active Map on Dragging window Click OK in the Preferences window Now the map is recontoured at the end of the drag, not at each step3 . Another, additional way to make the movements faster is to change the number of steps for the Smooth Recentering. Again you nd this in the Preferences (Preferences General Smooth Recentering). Change the Number of Steps from the default 80 to something smaller, e.g. 20. You can display the contacts too, as you do this: Select Measures from the Coot menu-bar Select Environment Distances. . . Click on the Show Residue Environment? check-button Also Click Label Atom? if you wish the C atoms of the residues to be labelled. Click OK in the Environment Distances window Click Apply in the Go To Atom window [You cant change the colour of the Environment distances] You can turn off the Environment distances if you like.
3 which

looks less good on faster computers.

Figure 5: Coots Go To Atom Window.

Figure 6: Coot showing Atom Label and environment distances.

2.8 Change the Clipping (Slab)

Select Draw from the Coot menu-bar Select Clipping. . . from the sub-menu

[Coot displays a Clipping window]

Adjust the slider to the clipping of your choice Click OK in the Clipping window Alternatively, you can use D and F4 on the keyboard, or Control Rightmouse up/down (Control Right-mouse left/right does z-translation).

2.9 Recontour the Map

Scroll your scroll-wheel forwards one click5

3 higher contour level] [Coot recontours the map using a 0.05electron/A

Scroll your scroll-wheel forwards and backwards more notches and see the contour level changing. If you dont have a wheel on your mouse you can use + and - on the keyboard. Note that the Scroll button in the Display Manager allows you to select which map is affected by this6 .

2.10 Change the Map Colour

Select Edit from the Coot menu-bar Select Map Colour in the sub-menu Select 1 xxx FWT PHWT in the sub-menu

[Coot displays a Map Colour Selection window]

Choose a new colour by clicking on the colour widgets

[Coot changes the map colour to match the selection ]

Click OK in the Map Colour Selection window

2.11 Select a Map

Select a map for model building: Menubar: Calculate Model/Fit/Rene... [Coot displays the Model/Fit/Rene window] Select Select Map. . . from the Model/Fit/Rene window
4 think: 5 dont

Depth of Field. click it down. 6 by default it is the last map, which is not necessarily the map that you want.

click OK (you want to select the map with . . . FWT PHWT) Alternatively you can use the modelling toolbar icon buttons (here Map) displayed on the right side of the Coot window. Most options found in the Model/Fit/Rene window are available here too. If you are not sure which icon corresponds to which function look at the displayed tips when over the button with the mouse. Or change the display style of the buttons by clicking on the bottom arrow and select another style to get only or additionally text displayed.

3 Model Building
So whats wrong with this structure? you might ask. There are several ways to analyse structural problems and some of them are available in Coot. Validate Density Fit Analysis tutorial-modern.pdb [Coot displays a bar graph] Look at the graph. The bigger and redder the bar the worse the geometry. There are 2 area of outstanding badness in the A chain, around 41A and 89A. Lets look at 89A rst - click on the block for 89A.

[Coot moves the view so that 89A CA is at the centre of the screen ]

3.1 Rotamers
Examine the situation. . . [ The sidechain is pointing the wrong way. Lets Fix it...] Menubar: Calculate Model/Fit/Rene...
7

[Coot displays the Model/Fit/Rene window]

Select Rotamers from the Model/Fit/Rene window 8 . In the graphics window, (left-mouse) click on an atom of residue 89A (the C, say)

[Coot displays the Select Rotamer window]

Choose the Rotamer that most closely puts the atoms into the side-chain density Click Accept in the Select Rotamer window

[Coot updates the coordinates to the selected rotamer]

Click Real Space Rene Zone in the Model/Fit/Rene window9 . In the graphics window, click on an atom of residue 89A. Click it again.

[Coot displays the rened coordinates in white in the graphics and a new Accept Renement window]
Click Accept in the Accept Renement window.

[Coot updates the coordinates to the rened coordinates. 89A now ts the density nicely.]
7 or use the modelling toolbar on the right of the Coot window, i.e. you dont need to open the Model/Fit/Rene window 8 Or click on the Rotamers button of the modelling toolbar 9 . . . or use the modelling toolbar button

OK. Thats good. Now, how about if we just use Real Space Renement only? Click Undo twice

[Coot puts the sidechain back to the original position]

Click Real Space Rene Zone in the Model/Fit/Rene window10 . In the graphics window, click on an atom of residue 89A. Click it again.

[Coot displays the rened coordinates in white in the graphics and a new Accept Renement window]
Now using left-mouse, click and drag on the intermediate (white) CZ atom of the PHE (if you mis-click the atom, the view will rotate). Can you pull the atom around so that the side-chain ts the density? [Yes, you can]

Figure 7: 89A now ts the density nicely.

3.2 More Real Space Renement

Now lets have a look at the other region of outstanding badness: Click on the graph block for 41 A

[Coot moves the view so that 41A CA is at the centre of the screen]
Examine the situation. . . Residue 41 is in a mess and not tting to the density. Can you x it? [Yes, you can] The trick is Real Space Rene that zone. So. . .
10 . . . or modelling

toolbar button

10

 You can either Real Space Rene a few residues (40, 41 and 42) or just 41. Take your pick. Click on Real Space Rene Zone in the Model/Fit/Rene window Select a range by clicking on atoms in the graphics window (either atoms in 40 then 42 or an atom in 41 twice)

[Coot displays intermediate (white) atoms]

Click and drag on some atoms until the atoms t nicely in the density. If you want to move a single atom then Ctrl Left-mouse to pick and move (just) that intermediate atom. [Note: Selecting and moving just the Carbonyl Oxygen is a good idea - use Ctrl Left-mouse to move just one atom.]

4 Blobology
4.1 Find Blobs
To be found under Validate (called Unmodelled Blobs). You can use the defaults in the subsequent pop-up. Press Find Blobs and wait a short while. You will get a new window that tell you that it has found unexplaned blobs. Time to nd out what they are. 4.1.1 Blob 3 Lets start from Blob 3 (the blobs are ordered biggest to smallest - Blobs 3 and 4 (if you have it) are the smallest). Click on Blob 3

[Coot centres the screen on a blob]

Examine the situation. . . [We need something tetrahedral there. . . ] Place Atom At Pointer on the Model/Fit/Rene window11

[Coot shows a Pointer Atom Type window]

SO4 in the new window. . . In the Pointer Atom Added to Molecule: frame, change New Molecule to tutorial-modern.pdb Click OK. Examine the situation. . . the orientation is not quite right. Lets Real Space Rene it (you should know what to do by now. . . ) (Real Space Rene Zone then click an atom in the SO4 twice. Accept)

[The SO4 ts better now].

Blob 4 is like Blob 3 (isnt it?)
11 also

available in the modelling toolbar

11

4.1.2 Blob 2 Click on the button Blob 2 and examine the density. Something is missing from the model. What? This protein and has been co-crystallized with its ligand substrate. Thats what missing: 3 GMP. So lets add it. . . File Get Monomer. . . Type 3GP in the box (Use Upper Case). Press return. . .

[Coot pauses for a few seconds while LIBCHECK and REFMAC run] [3GP appears]
It is generally easier to work without hydrogens, so lets delete them Delete. . . from the Model/Fit/Rene window 12 Hydrogens in Residue click on an atom in 3GP

[Hydrogens disappear]
The 3GP is displaced from where we want it to be. Rotate/Translate Zone from the Model/Fit/Rene window13 click on an atom in 3GP twice

[Intermediate (white) atoms appear]

Drag it or use the sliders to move the intermediate fragment to the approximately the right place. Click OK in the slider window Now optimize the t using Real Space Rene Zone like we did before. Now merge this ligand into the protein: Calculate Merge Molecules. . . Click (activate) monomer-3GP.pdb into Molecule: tutorial-modern.pdb Merge 4.1.3 Blob 1 Click on Blob 1 Examine the situation. . . What is this density? [We need to add residues to the C-terminus of the A chain.] The missing residues are GLU, THR, CYS (QTC).
12 Found 13 Found

in the modelling toolbar? Of course! it in the modelling toolbar?

12

 Calculate Fit Loop. . .

[Coot pops-ups a Fit Loop dialog]

Add residue number 94 to 96 in the A chain. The single letter codes of the extra residues are QTC Make sure that you can see the unmodelled density well, then click Fit Loop Watch. . . (fun eh?) Examine the density t.

[It should be ne, except at the C-terminus. We need to add an OXT atom to the residue]
Calculate Other Modelling Tools. . . Add OXT to Residue. . . Add it This is a far as I expect you to get.

5 Extra Fun (if you have time)

5.1 Waters
Fit waters to the structure Find Waters. . . in the Other Modelling Tools dialog 14 , then OK (using the defaults)

[Waters appear]
To check the waters: Click on Measures in the main menubar. Click on Environment Distances Click on the Show Residue Environment? check-button Change the distances as you like Use the Go To Atom widget to go to the rst water (probably towards the end of the list of residues in Chain W) Use the Spacebar to navigate to the next residue (and Shift Spacebar to go backwards) If you dont like the fast sliding15 you can turn it off (if you havent done so already): Click Edit Preferences. . . in the main menubar Click General Smooth Recentering... Click No
14 In older versions of Coot, the Find Waters button can be found in the Model/Fit/Rene dialog or the water drop in the modelling toolbar 15 its not very good for water checking

13

5.2 Working with NCS

The tutorial data has two-fold NCS. With good data it is interesting to investigate the differences between the NCS copies. This may be done by comparing the NCS related electron density, comparing the NCS related chains, or comparing the Ramachandran plots for related chains: Comparing the NCS related electron density. Go to Calculate/NCS maps and select the rst map and model. Now, if you go to anywhere in the A chain, you will see two sets of electron density - the original density for the A chain, and the density for the B chain transformed to overlap the A chain density. This gives you a visual comparison of any differences. Look at the density in the B molecule. Why does the density not agree here? (Hint: the NCS is not a 2-fold rotation in this case, it is improper). Comparing the NCS-related chains. Go to Draw/NCS ghost control and select Draw non-crystallographic ghosts. You will now see a copy of the B chain superimposed on the A chain. The B chain is draw using thin bonds. Look for regions where the models differ. Using the NCS maps tool, check that the differences in the models are supported by the density. Compare the NCS-related chains using NCS jumping. This is an alternative way of examining NCS similarities and differences. Use the Display Manager to undisplay the NCS maps you recently created above. Use the Goto Atom dialog and press the Update from Current Position button.

[Coot shifts the centre of the screen to the closest displayed CA atom]
Identify the chain that you are looking at (for example, by double-clicking on an atom) Now press the o key on the keyboard.

[Coot shifts the centre of the screen to a NCS-related chain]

Identify the chain that you are looking at now. Press o again. What is happening? (Note: o stands for Other NCS-related chain.) Comparing the Ramachandran plots for related chains. Go to Validate/Kleywegt plot. Check the Use specic chain options and select chains A and B. You will get a Ramachandran plot with equivalent residues from the A and B chains linked by arrows. Long arrows indicate signicant differences. Click on a dot to view the residue concerned. Another tool for identifying NCS differences is the Validate/NCS differences graph. This gives a clickable histogram of differences.

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5.3 Add Terminal Residue

[To be found on the Model/Fit/Rene dialog16 ] Use the Go To Atom window to go to residue 72 A. What do you see? [You see missing atoms (that is, you dont see them). This residue is supposed to be a CYS! Bad things have happened to it. Lets get rid of this residue. ] [There may also be waters in the side-chain positions too (they have to be removed too).] Delete. . . (Make sure Residue/Monomer is active) Click on an atom of residue 72 A.

[Residue 72 A disappears]
Lets put back an ALA. Add Terminal Residue. . .

[Coot adds intermediate white atoms and pops up a dialog]

Accept the new atoms OK, we now have a ALA. We want a CYS: Mutate & Auto Fit. . . Click on an atom in the new ALA

[Coot pops up a residue type chooser]

Choose residue type CYS

[Coot mutates and ts a CYS]

Examine the situation. [ There is an extra blob of density on that CYS. What is it?] It is an alternative conformation. Lets model it Add Alt Conf. . .

[Coot pops up a residue splitter dialog]

Choose how you want to split your residue (the Right Way is an unresolved philosophical issue. . . 17 ) Click on an atom in 72 A

[Coot adds intermediate white atoms and pops up a Rotamer Chooser]

Choose the correct rotamer - it shouldnt be difcult to tell which is the closest. Accept when you are happy with you choice.
16 and 17 Actually

in the modelling toolbar Jane Richardson may disagree with that statement.

15

 Now optimize the t of this new residue with Real Space Renement. The renement of each alternate conformations is independent. Real Space Rene Zone click on (say) SG,B of 72A Press A (on the keyboard)

[Coot moves the atoms a bit]

Accept Now do the same with the other conformation. [Ahhh! Much better.]

5.4 Display Symmetry Atoms

To be found on Draw Cell & Symmetry menu item in the main menu. Try: Show Symmetry Atoms? Yes Symmetry as Calphas? [on] Colour symmetry by molecule [on] Symmetry Radius 30A Colour Merge 0.1 Show Unit Cell? [on] OK Zoom out and have a look at how the molecules pack together.

5.5 Skeletonization and Baton Building

You can calculate the map skeleton in Coot directly: Calculate Map Skeleton... On. This can be used to baton build a map. You can turn off the coordinates and try it if you like (the Baton Building window can be found by clicking Ca Baton Mode. . . in the Other Modelling Tools dialog18 . If you want to do this, I suggest you use Go To Atom and start residue 2 A (this allows you to build the complete A chain in the correct direction (it takes about 15 minutes or so) and you can compare it to the real structure afterwards. Remember, when you start, you are placing a CA at the baton tip and at the start you are placing atom CA 1. This might seem that you are double-backing on yourself - which can be confusing the rst time.
18 this

is quite advanced)

16

5.6 Rene with Refmac

Refmac is a program that does Maximum Likelihood renement of the model, and the interface to it can be found on the Model/Fit/Rene dialog. (By default there is no icon on the toolbar for this action - open the window from the calculate menu19 ). Now click on Run Refmac. . . (at the bottom of the Model/Fit/Rene window). The defaults should be ne... Run Refmac in the new window. . . . . . Wait. . . [The cycle continues. . . ] Use Validate Difference Map Peaks to nd interesting features in the newly created map and model. Python enabled version only: a dialog with geometric outliers and other interesting things (if they exist) detected by Refmac shows up 20 .

6 Use the EDS

Lets validate a structure deposited in the PDB. Use a web browser and go to http://eds.bmc.uu.se/eds/. Use the keyword search to nd the structure of a particular protein/ligand/author. File Get PDB and Map Using EDS Get the accession code and paste it into the entry box that pops up. Use the validation tools in Coot to examine how good a PDB le this is... [the Difference Map Peaks can be interesting]

6.1 Make a (Pretty?) Picture

(Depends on the appropriate supporting software being available): Arrange a nice view Press F8 Wait a few seconds. . .

Colophon
A This document is written using XEmacs 21.5 in L TEX using AUCTEX and is distributed with the Coot source code.

19 or add your own Run Refmac button to the toolbar or the main/top toolbar. To add the button to the modelling/side toolbar, open the Preference window. Now go to Preferences General Renement Toolbar. In the right hand window scroll down and tick the box besides Run Refmac. . . . A corresponding button will appear on the modelling toolbar. Alternatively you can add your own Run Refmac. . . button to the top toolbar of the Coot window (only in Python versions). Click Rightmouse on the toolbar (besides the Display Manager button) and you will see a pop-up menu. Select Manage Buttons, tick the box besides Add Alt Conf and click Apply. A new button named Add Alt Conf will appear on the toolbar. 20 This is an analysis from the Refmac log le and can alternatively be opened from Extensions... Rene... Read REFMAC log

17