1. An Introduction To The ICM Graphical User Interface

2. Upper toolbars/ menus Lower toolbar/ menus Side toolbar Workspace panel Command line terminal HTML documents 3D graphics window MAIN ICM COMPONENTS

3.  The 3D window has several ‘hot-zones’ (marked as red boxes in the figure), which provides access to operations that change the scene’s view; Move the cursor into one of these zones to change the dragging function of your mouse.  All the functions described below assumes clicking + holding on the button indicated (i.e. dragging): move = rotation up/down = zoom in/out up/down = clip back plane up/down = clip front plane up/down = clip back+front planes Left button move = selection (markers appear); select empty zones to remove selection Right button move = translation Middle button Works while the cursor is on ‘rotation’ mode 3D Graphics Window Shortcuts

4. A. Loading molecules (2 ways): A. Loading molecules (2 ways): 1. drag&drop the PDB file into workspace or 2. File  Load  PDB  PDB Type in the PDB code Check this option Uncheck these two options & press OK B. Converting to ICM format: B. Converting to ICM format: 1. right-click on an object and pick ‘Convert PDB’ 2. On the following dialogue, uncheck all the boxes and press ‘OK’ Load a PDB File

5. Clicking here turns everything under it on, using the default settings (i.e. amino-acid chains as ribbons, ligands as xsticks, ions as CPK, etc.) Clicking here turns only this chain (molecule level) on. Displaying a Structure

6. 2. Click here. Ribbons representation of the chain (chain a) will appear. Many green crosses representing the components of the selection will appear as well. Each shows you an atom within the selection. 3. Click here to clear the selection (and get rid of the green crosses) 1. Double-click the text; background of the line will turn grey Displaying Structures

7. 1. Left-click + hold will open a menu providing other options (shown here) Left-click to add a slide immediately after the presently active (slide ‘2’ will be added in this example). Last slide (click to display) Current slide (pull menu to choose) First slide (click to display) Slide navigation buttons (previous/ next) Slide layout button 2. Pick ‘save slide’ for extra options when saving slides Saving Slides

8. Type in the name of the slide. Normally a few descriptive words such as ‘active site’, ‘mutation’, ‘alternate loop conformation’, etc. Check this box if you are preparing the ‘default’ slide or any other slide where the windows distribution is different from the slide-mode. Check both transition effects boxes for an iSee slide and change the values to the ones shown in the picture (2000 ms for smooth; 1000 ms for blend). \ Finish with the OK button. The position in the stack (order) where the new slide should be inserted can be defined here. Saving Slides

9. Selection levels (4 levels)Selection modes (4 modes) Representation modes (6 modes) Selections and Representations

10. You can expand protein/ peptide chains to see the residues by clicking on the ‘+’ sign by the chain. Then left-click + drag to select residues. You can add non- contiguous residues by holding ‘CTRL’ key while selecting. If there are elements being displayed, you can also select in the graphic window directly. Either change to the selection tools or with your mouse in ‘rotation’ mode, right-click + hold + drag to add to your selection. Selections and Representations

11. Find your ligand and right-click to launch the menu – then pick ‘ligand pocket’. This will automatically generate the pocket (surface) surrounding the selected molecule. To display labels, side chains and hydrogen bonds, check the box on the following dialogue box. Pocket is displayed as a 3D mesh - (representation mode can be changed by right-click on the mesh display box) If made from a converted PDB, pocket will be coloured (green: aliphatic, blue: HB donor; red: HB acceptor) Active Site Ligand Pocket

12. Find your ligand and right-click to launch the menu – then pick ‘extract ligand(s)’. You’ll be offered option to extract as 2D or 3D. Pick 2D and a table will be generated with the ligand(s). On the new table, right-click on the compound and on the menu pick ‘save/export image’. You can then copy the image to an internal album or save it as a image to be used in other programs (e.g. Powerpoint). Extract Ligand

13. Make a selection (see previous sections) and click on either the residue or atom label buttons. If the position of the label needs to be changed, click and hold on the label button and check ‘drag labels’. This activates the dragging hotspot on every label: Adding Labels

14. Pre-defined colours: Right-click = to set the background colour Left-click = to set the representation colour ! Warning: left-clicking when there is no selection = everything displayed will be coloured. Pre-defined colours: Right-click = to set the background colour Left-click = to set the representation colour ! Warning: left-clicking when there is no selection = everything displayed will be coloured. Colour wheel: preset colouring schemes – applied to the selection (if no selection, will be applied to everything displayed in the screen) Some useful schemes: - NtoC: from N- to C-terminus of a protein, starting as blue and changing to red. - Bfactor: maps the B-factors (when available) to the structure (low=blue; high=red) - Chain: automatically assigns a different colour for each chain Colour wheel: preset colouring schemes – applied to the selection (if no selection, will be applied to everything displayed in the screen) Some useful schemes: - NtoC: from N- to C-terminus of a protein, starting as blue and changing to red. - Bfactor: maps the B-factors (when available) to the structure (low=blue; high=red) - Chain: automatically assigns a different colour for each chain Coloring

15. For any of the representation button, left-click and hold to be presented with additional options – colour amongst them. The colour tool is exactly the same as the one shown above. Note that the colour will apply to the selection AND the chosen representation only. If nothing is selected, then everything being displayed using the chosen representation will be coloured. For any of the representation button, left-click and hold to be presented with additional options – colour amongst them. The colour tool is exactly the same as the one shown above. Note that the colour will apply to the selection AND the chosen representation only. If nothing is selected, then everything being displayed using the chosen representation will be coloured. Coloring According To Properties

16. 2. Right-click on any of the green selection crosses and pick the ‘annotate selection’ option. 3. Type in the site tag name (and optionally a longer description – not recommended: tends to clutter the screen). 5. Tag hot spot 2: Middle-click + drag: moves the head of arrow (in 3D space) 5. Tag hot spot 2: Middle-click + drag: moves the head of arrow (in 3D space) 4. Tag hot spot 1: Left-click: cycles through site description modes. Middle-click + drag: moves the end of arrow (in 3D space). 4. Tag hot spot 1: Left-click: cycles through site description modes. Middle-click + drag: moves the end of arrow (in 3D space). 1. Make a selection of residue(s) Single residue: right-click over residue. Multiple res.: right-click + hold + drag to select, then right-click on the selection to activate menu. 1. Make a selection of residue(s) Single residue: right-click over residue. Multiple res.: right-click + hold + drag to select, then right-click on the selection to activate menu. Adding Sites

17. 1. Start by preparing the representation. Anything 3D on the screen will be captured (ribbons, sticks, CPK, skins, other meshes, etc.). Text will not be captured. The orientation doesn’t matter: the grob to be generated will be a 3D object, so it can be reposition it later. ! Make sure that all elements to be captured in the grob are visible on-screen. 1. Start by preparing the representation. Anything 3D on the screen will be captured (ribbons, sticks, CPK, skins, other meshes, etc.). Text will not be captured. The orientation doesn’t matter: the grob to be generated will be a 3D object, so it can be reposition it later. ! Make sure that all elements to be captured in the grob are visible on-screen. 2. Enter the following command in the terminal: make grob image 2. Enter the following command in the terminal: make grob image Meshes – Graphical Objects (Grob)

18. In the command line window, a message will be displayed giving the name of the new grob. Change it as soon as it is created to allow you to track them. Right-click on the name of the newly-created grob, pick ‘rename’ from the menu and then type the new name In the command line window, a message will be displayed giving the name of the new grob. Change it as soon as it is created to allow you to track them. Right-click on the name of the newly-created grob, pick ‘rename’ from the menu and then type the new name Check the result: undisplay everything and right- click on the square in front of your new grob. Representation styles available: dot, wire (wireframe), smooth surfaces, rugged surfaces and transparent smooth surfaces. Wire and transparent surfaces are useful if you want to show what’s underneath. Check the result: undisplay everything and right- click on the square in front of your new grob. Representation styles available: dot, wire (wireframe), smooth surfaces, rugged surfaces and transparent smooth surfaces. Wire and transparent surfaces are useful if you want to show what’s underneath. Meshes – Graphical Objects (Grob)

19. Without occlusionWith occlusion Occlusion shading adds shadow according to accessibility: the less accessible, the darker the shadow. Right-click on the mesh and pick ‘occlusion shading’ from the options. A new dialog appears - change the value to determine the level of shading. Occlusion shading adds shadow according to accessibility: the less accessible, the darker the shadow. Right-click on the mesh and pick ‘occlusion shading’ from the options. A new dialog appears - change the value to determine the level of shading. Meshes – Graphical Objects (Grob)

20. 1. In the workspace, identify the ligand to be shown with elec. density and double-click on it to select it: 2. tools  Xray  Contour Electron Density 1. In the workspace, identify the ligand to be shown with elec. density and double-click on it to select it: 2. tools  Xray  Contour Electron Density 3. In the new dialogue box, pull down to select the EDS map. 4. Correct the sigma level for density contouring to 1.0. 3. In the new dialogue box, pull down to select the EDS map. 4. Correct the sigma level for density contouring to 1.0. Start loading an electron density map – a.Tools  Xray  Get Electron density map... or b.Drag & drop a CCP4 format density map into the workspace Electron Density

21. 5. A new mesh with the density has been created, but all the density around the ligand is also displayed – you might want to clear that up a bit and display only density for the ligand. 6. To do so, right-click on the density mesh  split 5. A new mesh with the density has been created, but all the density around the ligand is also displayed – you might want to clear that up a bit and display only density for the ligand. 6. To do so, right-click on the density mesh  split ICM will now take the mesh and look for continuity. Everything that is continuous will be separated as a new mesh. 7. The results are sorted according to size. Normally your ligand’s density is the largest, so enter a low number in the split dialogue box. ICM will now take the mesh and look for continuity. Everything that is continuous will be separated as a new mesh. 7. The results are sorted according to size. Normally your ligand’s density is the largest, so enter a low number in the split dialogue box. Electron Density

22. 8. now that the main mesh has been split, click on each one of the new meshes to find the one that wraps around your ligand. Your scene is much cleaner now. Electron Density

23. 1. Display both molecules in the screen. 2. Select both molecules (you’ll see green crosses). 3. Click on the ‘superimpose’ button. Superimpose

24. 1. Superimpose works only on the object/ molecule level. It doesn’t affect meshes. However when a superimpose is performed, ICM stores the transfrmation matrix into the variable ‘R_out’. 1. Superimpose works only on the object/ molecule level. It doesn’t affect meshes. However when a superimpose is performed, ICM stores the transfrmation matrix into the variable ‘R_out’. 2. In the terminal, enter the following command: transform R_out Note: the command needs to be executed immediately after the superimpose operation (otherwise the R_out variable might be updated with output from other operations). 2. In the terminal, enter the following command: transform R_out Note: the command needs to be executed immediately after the superimpose operation (otherwise the R_out variable might be updated with output from other operations). Transpose

25. 1. Right-click in the HTML document and select the ‘edit’ option. There are two ways of starting a HTML document: 1. Drag&drop an external HTML file in the workspace 2. Open a new one with File  New  Pick the ‘HTML’ tab 3. Type in a title for your annotation/ HTML document; check the ‘pop in Brwoser’ option and finalise with ‘OK’. 4. Right-click in the HTML document and select the ‘edit’ option. If you have started a new one from scratch, then the content will be blank. Adding Text in the HTML Editor

26. 2. The usual text editor tools will appear. At the same time, the main window is ready to accept typed or pasted text / elements. 3. If the panel is too narrow, some of the tools will be hidden. These can be accessed by resizing the HTML panel or by clicking on this button 4. When you re done, remember to save the modifications. Note: this save operation saves the HTML within the ICM project, but is not saving the entire project (with all the loaded elements, etc.). Adding Text in the HTML Editor

27. 1. Right-click anywhere on a HTML document  edit to start the HTML editor 2. Locate the text to have an ICM link added to it and select it (left-click hold + drag). 3a. On the selected text, Right-click  Insert  Insert Slide and a new dialog will open. 3b. Alternatively click the little camera icon on the HTML editor icons bar. 2. Locate the text to have an ICM link added to it and select it (left-click hold + drag). 3a. On the selected text, Right-click  Insert  Insert Slide and a new dialog will open. 3b. Alternatively click the little camera icon on the HTML editor icons bar. Linking Text To Slides

28. 2. Use the pull down menu to pick the desired slide. 3. Select and delete the word ‘smooth’. 4. Finish with ‘OK’. Your text has been now linked to the selected slide. 1. Pick the ‘Slide’ tab. 3. Pick now the ‘ICM script’ tab. Linking Text To Slides

29. Simply click on the save button to save. Usual saving options (e.g. Save as, etc.) will be made available in the dialogue box that opens. Everything loaded into ICM and created during your session (a ‘project’) can be bundled into a single ICM binary file (extension.icb ). The.icb file can now be used by any version of ICM, running in any of the supported Operating Systems and also as a web-browser plug-in. For downloads of the programs and plug-ins, please visit: http://www.molsoft.com Saving a Project