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Coot Tutorial CCP4 Workshop Bangalore March 23, 2005 Contents 1 Mousing . . . . . . . . . . . . . . . . . . . . . . 2 Introductory Tutorial . . . . . . . 2.1 Get the ﬁles . . . . . . 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 3 3 4 4 6 7 8 8 8 8 . 9 . 10 10 . 10 . 10 . 11 . 12 12 . 12 . 12 . 13 . 13 . 13 3 Model Building 3.1 Rotamers . . . . . . . . 3.2 More Real Space Reﬁnement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 Blobology 4.1 Find Blobs . . . 4.1.1 Blob 3 . 4.1.2 Blob 2 . . . . . . . . . . . . . 4.2 Make a (Pretty?) Picture . . . . . . . . . . . 5 Extra Fun (if you have time) . . . . . . . . 5.1 Waters . . . . 5.2 Add Terminal Residue . . . 5.3 Mutate Residue . . . . . . . 5.4 Display Symmetry Atoms . 5.5 Reﬁne with Refmac . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

1 Mousing First, how do we move around and select things? Rotate view Left-mouse Drag Translates view Ctrl Left-Mouse Drag Label Atom Shift Left-Mouse Zoom in and out Right-Mouse Drag Centre on atom Middle-mouse Increase map contour level Scroll-wheel Forward Scroll-wheel Backward 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 reﬁne residue 2.1 Get the ﬁles The files are already in the "tutorials" folder 2.2 Start Coot Before you start coot, you need to setup the proper environment. This is currently done by “sourcing” a setup ﬁle. The location of this setup ﬁle is system dependent, For the LMB tutorial To then use coot, simply type (in the X11 window) % source /Users/vis/.cshrc %coot When you first start coot for this tutorial, you may see a message saying that there is an "auto-save" file and asking if you want to use it. For the purpose of this tutorial, click on "No" to answer this question. When you ﬁrst start coot, it should look something like Figure 1. 2

Figure 1: Coot at Startup Not much to see at present... Actually, from now coot screenshots will be displayed with a white background, whereas you will see a black one 2.3 Display Coordinates So let’s read in those coordinates: Select “File” from the Coot menu-bar1 Select the “Open Coordinates” menu item [CootdisplaysaCoordinatesFileSelectionwindow] For the LMB tutorial, the files you need will be in: /Users/vis/tutorials/coot Either – Select tutorial.pdb from the “Files” list or – Type demo.pdb in the Selection: entry Click “OK” in the Coordinates File Selection window [CootdisplaysthecoordinatesintheGraphicsWindow] 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 don’t like this. So you might like to try the following: In the Coot main menu-bar: HID Virtual Trackball Flat (Use the “Spherical Surface” option to turn it back to how it is by default) 1Note you can also use “Alt-F” instead of clicking on “File” 3

Figure 2: Coot After Loading Coordinates 2.5 Display maps We are at the stage where we are looking at the results of the reﬁnement. The reﬁnement programs stores its data (labelled lists of structure factor amplitudes and phases) in an “MTZ” ﬁle. Let’s take a look. . . Select “File” from the Coot menu-bar Select “Auto Open MTZ” menu item [CootdisplaysaDatasetFileSelection window] Select the ﬁlename rnasa-1.8-all refmac1.mtz If you choose instead “Open MTZ, cif or phs...” you will see: [CootdisplaysaDatasetFileSelectionwindow] Select the ﬁlename rnasa-1.8-all refmac1.mtz [CootdisplaysaDatasetColumnLabelSelectionwindow] Notice that you have a selection of different column labels for the “Ampli- tudes” and “Phases”, however, let’s use the defaults: “FWT” and “PHWT”. Press “OK” in the Column Label Window Now open the MTZ ﬁle 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. 2or up-to-down, if you prefer that 4

Figure 3: Coot MTZ Column Label Selection Window Figure 4: Coot after reading an MTZ ﬁle and zoomed in. 5

2.7 Recentre on Different Atoms Select “Draw” from the Coot menu-bar Select “Go To Atom. . . ” [CootdisplaystheGoToAtomwindow] Select “1 A 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” “Space”in the graphics window) to move along the chain. Click Middle-mouse over an atom in the graphics window [Cootrecentresonthatatom] Ctrl Left-mouse & Drag moves the view around. If this is a too slow and jerky: – Select Draw from Coot’s menu-bar – Select the “Dragged Map. . . ” menu item – Select “No” in the “Active Map on Dragging” window – Click “OK” in the “Active Map on Dragging” window Now the map is recontoured at the end of the drag, not at each step3. Figure 5: Coot’s Go To Atom Window. 3which looks less good on faster computers. 6

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 Figure 6: Coot showing Atom Label and environment distances. You can turn off the Environment distances if you like. 2.8 Change the Clipping (Slab) Select “Draw” from the Coot menu-bar Select “Clipping. . . ” from the sub-menu [CootdisplaysaClippingwindow] Adjust the slider to the clipping of your choice Click “OK” in the Clipping window Alternatively, you can use “D” and “F”4 on the keyboard. 4think: Depth of Field. 7

2.9 Recontour the Map Scroll your scroll-wheel forwards one click5 [Cootrecontoursthemapusinga0.05electron/˚A highercontourlevel] Scroll your scroll-wheel forwards and backwards more clicks and see the contour level changing. 2.10 Change the Map Colour Select “Edit” from the Coot menu-bar Select “Map Colour” in the sub-menu Select “0 xxx FWT PHWT” in the sub-menu [CootdisplaysaMapColourSelectionwindow] Choose a new colour by clicking on the colour widgets [Cootchangesthemapcolourtomatchtheselection] Click “OK” in the Map Colour Selection window 2.11 Select a Map Select a map for model building: Menubar: Calculate Model/Fit/Reﬁne... [CootdisplaystheModel/Fit/Reﬁnewindow] Select “Select Map. . . ” from the Model/Fit/Reﬁne window click OK (you want to select the map with “. . . FWT PHWT”) 3 Model Building “So what’s wrong with this structure?” you might ask. There are several ways to analyse structural problems and some of them are available in Coot. Validate [Experimental] Geometry Analysis tutorial.pdb Look at the graph. There are 2 area of outstanding badness in the A chain, around 41A and 89A. Let’s look at 89A ﬁrst - click on the block for 89A. [Cootmovestheviewsothat89ACAisatthecentreofthescreen] 5don’t click it down. 8

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