Cn3D ,RasMol and SPDbv in homology modeling-case studies



            This is a tutorial for Cn3D. It is intended as a guide to the major features of Cn3D for both new and experienced users. New users may wish to learn to use the program by reading this document in order; experienced users may wish to jump to sections of particular interest using the above index and hyperlinks within the text.

This tutorial is not an exhaustive explanation of all the program's features; there is a built-in help document that explains Cn3D's user interface and features in detail. To access it, launch the Cn3D program, then select the menu option for Help:Commands.  

What does Cn3D do?           
            Cn3D is a visualization tool for biomolecular structures, sequences, and sequence alignments. What sets Cn3D apart from other software is its ability to correlate structure and sequence information: for example, a scientist can quickly find the residues in a crystal structure that correspond to known disease mutations, or conserved active site residues from a family of sequence homologs. Cn3D displays structure-structure alignments along with their structure-based sequence alignments, to emphasize what regions of a group of related proteins are most conserved in structure and sequence. Also included are custom labeling features, high-quality OpenGL graphics, and a variety of file exports that together make Cn3D a powerful tool for literature annotation. Cn3D is typically run from a WWW browser as a helper application for NCBI's Entrez system, but it can also be used as a standalone application.
With version 4, Cn3D is now a complete multiple alignment editor as well, and includes algorithms for aligning sequences to other sequences and to structures. You can now create and even annotate multiple alignments. Cn3D is used as the primary alignment curation tool for the CDD project.

 Downloading and installing Cn3D
            Cn3D is available for Windows, Macintosh, and various UNIX platforms. These pages include instructions for downloading and installing Cn3D, and for configuring WWW browsers to use Cn3D as a helper application.

Document conventions         
            Screen shots of the Cn3D and sequence windows are provided at various intervals to exemplify the concepts described; they will appear as thumbnail images linked to full-size screen shots. Note that the full-size images are stored in PNG format - depending on the browser used, a PNG-capable helper application may be required to view them. The Windows version of Cn3D was used to create these images, but aside from platform look-and-feel differences in user interface and window borders, the images will look largely the same on any platform.
When referring to specific elements of the user interface (pull down or popup menus, buttons, etc.), this document will use boldface type with colons separating the ordered mouse-actions needed to access that feature. For example, Style:Edit Global Style:Details:Tube Radius means go to the "Style" pull-down menu (in the structure window), select the "Edit Global Style" item. A tabbed control panel comes up; select the "Details" tab, then look for the "Tube Radius" control.           

Viewing individual structures in Cn3D:    

            This chapter uses as its example the 1D5R PDB structure; see the previous chapter for instructions on how to retrieve the data for it.

Basics of Cn3D controls      
            While not intended as a comprehensive reference for Cn3D's user interface, this section provides a basic overview of the program's controls, and illustrates techniques for visualizing different scientific aspects of the data:
•           the structure window main menu
•           the style panel
•           some examples using custom settings
•           Cn3D's sequence viewer
For additional information about all the program's features, there is a built-in help document that explains Cn3D's user interface and features in detail. To access it, launch the Cn3D program, then select the menu option for Help:Commands.       

The structure window main menu 

            The File menu controls the input of data into Cn3D, and output to a variety of data and image file types; these are fairly self-explanatory. In particular, the File:Save action saves the structure along with the current view, drawing settings, and any user annotations, so that work can be saved and retrieved. The File:Export PNG item saves the contents of the structure drawing area to a PNG format image file for use in web pages or publications (like this tutorial!).

The View menu contains items that control how the structure as a whole is displayed. The whole structure can be made larger or smaller with View:Zoom In and View:Zoom Out, and the view returned to its original size and orientation as stored in the data file with View:Restore. View:Reset will fit the entire structure into the window. If there is more than one structure being viewed (e.g. a VAST alignment), or if the structure contains multiple models (e.g. an NMR structure, downloaded with all models), then each structure will be assigned its own "frame." The various View:Frame items control which frame is currently displayed. View:Animation is discussed in a later chapter.

The Show/Hide menu contains operations that allow certain substructures to be shown or hidden. The Show/Hide:Pick Structures dialog lets you choose which individual structures, chains, and domains are turned on or off. The other items in the Show/Hide menu are more relevant to alignment views.
The choices in the Style menu affect the shape and color of the different parts of the structure. For example, the default display for single structures is a combination of Style:Rendering Shortcuts:Worms and Style:Coloring Shortcuts:Secondary Structure which shows a worm backbone, no side chains, and solid objects - arrows and cylinders - to represent strands and helices. The colors are green for helices, strands orange, and coil blue.  (The location and extent of these secondary structure elements is determined by NCBI, and does not represent the helix and strand notations in the original PDB file.) Note that the arrows on the strands (and optionally on helix cylinders) always point in the N-to-C direction. The best way to learn what the other different styles are is simply to try them out!
Cn3D intentionally keeps color separate from drawing style. The Style:Coloring Shortcuts menu choices determine what properties are used to map different parts of the structure to different colors. Using these options, one can easily visualize a structure's NCBI-determined domain composition (Domain), or crystallographic temperatures (Temperature) from the PDB data, etc. TheStyle:Rendering Shortcuts choices determine the shape of the various parts of the structures, like Worms or Ball and Stick.           

The style panel          

            The style panel (Style:Edit Global Style) contains detailed controls for all drawing styles, colors, and labels, and is where much of Cn3D's flexibility is contained. In fact, all of the options in theStyle:Rendering Shortcuts and Style:Coloring Shortcuts menus are simply convenient shortcuts to different combinations of options in the style panel.
           The style panel's Settings tab has four columns of settings for the various structure elements identified on the left; these settings are applied globally to all structures. "On/Off" controls whether the elements are displayed (as well as what type of backbones are used), "Rendering" controls the geometry used to render the elements, and "Color Scheme" controls the elements' colors. Most of these can be set independently, with the exception that worm style can only be used for virtual backbones. The rightmost "User Color" column can be used to set colors for structural elements when the "User Selection" color scheme is chosen. The overall background color is also set this way.

The style panel's Label tab controls labeling of backbones, chain termini, and ions. (The actual fonts used are set from the File:Set Fonts controls in the structure window.) 

The style panel's Details tab allows specific control of some geometric properties of the rendering. For example, the Details:Worm tube radius setting controls how thick the worm backbone is when a worm display is chosen.

The Style:Annotate panel is discussed separately in the annotation chapter, but briefly, allows one to set different styles and labeling for specific user-selected residues, to set them apart from the rest of the structure.
Lastly, the File:Preferences:Quality tab controls the "quality" of the OpenGL rendering. All seemingly smooth and rounded objects in OpenGL are actually constructed out of many small flat polygons. The controls on this panel determine how fine a mesh of smaller polygons is used to construct the larger objects. The popup menus give detailed settings, while the three buttons on the right are a convenience to adjust the menus to predetermined settings. There is a tradeoff between the apparent smoothness of the objects and the speed at which they are rendered: more and smaller polygons give an object a nicer rounded appearance, but take longer to draw. Thus on an older computer, a lower quality setting may be necessary for Cn3D to respond quickly enough to be useful interactively. Conversely, on a fast computer, or for saving a prettier picture as a PNG image where speed is not an issue, a high quality setting may be preferable. You can also choose between orthographic and perspective projections.

Some examples using custom settings

Here is an image saved by File:Export PNG. This is PDB entry 1D5R, showing a close-up of the inhibitor in the active site, with element-colored wireframe sidechains, temperature-colored worm backbone, secondary structure-colored 3-d objects, and PDB-numbered labels every 5 residues. These are all set up in the Style:Edit Global Style panel.

To the right of the image is a link to a datafile of the same structure saved by File:Save. Clicking on this link will bring the structure up in Cn3D, with the initial view the same as the static image file. So for example, the user can zoom out (View:Zoom Out or View:Reset) to see how the surface of the protein has a higher temperature (more motion in the crystal) than the tightly packed core region. This demonstrates how Cn3D can be used to create and view interactive figures in a digital publication; see the annotation chapter for more on this topic.

  ... and click here to launch this figure in Cn3D

Here is another view of the same protein, with a wireframe backbone colored by secondary structure, 3-d objects colored by domain, and (partially transparent) solvent.

  ... and click here to launch this figure in Cn3D

Cn3D's sequence viewer      
            When a single structure is loaded into Cn3D, the sequence viewer shows the sequences of all protein and nucleic acid chains in the structure. The color of each residue is coordinated between the structure and sequence windows: each letter of the sequence represents a residue in the structure, and always adopts the color of the backbone's alpha carbon (or phosphorus, for nucleotides), even if side chains are colored differently from backbone in the structure window.
The most powerful application of the sequence window in Cn3D is to allow easy correlation of residues in the sequence with atoms in the structure. This is accomplished by highlighting - just as with a text editor, click-dragging the mouse across a region in the sequence window will cause the letters to "light up", and will apply the same highlight color to the corresponding atoms in the structure window. And the converse is true as well: double-clicking a residue in the structure window will cause it and the corresponding letter in the sequence window to light up.
Thus, the user can quickly locate and highlight interesting parts of the protein from the sequence window, like a cluster of active site residues. For example, here is 1D5R after highlighting some of the key catalytic and binding residues (as identified in Lee et al., 1999):

Note that there are two numbers - sequence location and PDB-assigned - shown for the residues when the mouse is moved over the sequence. This is because the crystallized protein is partially truncated, and other highly disordered residues are left out of the refined structure; these missing regions are not displayed in the sequence (e.g. by gap characters or some other graphic device), but are accounted for in the PDB's numbering scheme. See the alignment chapter, though, for a clever way to get around this problem!          


RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank. It was originally developed by Roger Sayle in the early 90s .
Historically, it was an important tool for molecular biologists since the extremely optimized program allowed the software to run on (then) modestly powerful personal computer. Before RasMol, visualization software ran on graphics workstations that, due to their expense, were less accessible to scholars. RasMol has become an important educational tool as well as continuing to be an important tool for research in structural biology.
RasMol has a complex version history. Starting with the series of 2.7 versions , RasMol is licensed under a dual license (GPL or custom licenseRASLIC).
RasMol includes a language (for selecting certain protein chains, or changing colors etc). Jmol and Sirius has incorporated the RasMol scripting language into its commands.
Protein Databank (PDB) files can be downloaded for visualization from members of the Worldwide Protein Data Bank (wwPDB). These have been uploaded by researchers who have characterized the structure of molecules usually by X-ray crystallography , NMR spectroscopy or electron microscopy.

Inter-process Communication

On UNIX platforms Rasmol can communicate with other programs via Tcl/Tk. Under Microsoft Windows, Dynamic Data Exchange (DDE) is used.
§                    multiple alignment program. The responsible Java class can be freely used in other applications.


  1. Basic Instructions (using the menus):
    1. To open a file: File/Open from within RasMol. From within Netscape, click on a RasMol viewable molecule (a .pdb file). (RasMol should automatically start and load in the molecule.)
    2. To open multiple files (i.e., can view up to 5 molecules simultaneously): File/Open (for each file, without closing the previous files) from within RasMol. From within Netscape, just click on another RasMol viewable molecule.
    3. To select a molecule: Click on molecule name in the Molecules window (the secondary window)
    4. To close a file (a molecule): File/Close when the molecule is selected.
    5. Moving the molecule(s):
button (Click & Hold)
Mouse button (Click & Hold)
button (Click & Hold)
<OpenApple> and 
mouse button
<alt><SHIFT> and 
left-mouse button
<SHIFT> and 
mouse button
<alt><SHIFT>and right-mouse button
<option><SHIFT> and 
mouse button
    1. To change to different representations (i.e., CPK, stick, ribbon, etc.): Display/Stick
    2. To determine distances, angles, dihedral angles:
      1. Click on appropriate icon in the Molecules window (the secondary window)
      2. Click once on the appropriate number of individual atoms. (With angles, clicking on atoms must be in the appropriate order.)
    3. To rotate bond (Note: This changes the angle.):
      1. Click on rotate angle icon in the Molecules window (the secondary window)
      2. Click on 2 atoms
      3. Click on rotate angle icon in the Molecules window (the secondary window) again
      4. Click on 3rd atom
      5. Use mouse button to rotate
    4. To color molecule in different ways:
      1. To color by the protein-secondary structure: Colours/Structure
        •  -helices: magenta
        •  -sheets: yellow
        • turns: pale blue
        • all other residues: white
      2. To color by residue type (i.e., each type of residue is colored a specific color): Colours/Shapely
      3. To color by atom type (below are the default colors): Colours/CPK
        • Carbon: gray
        • Hydrogen: white
        • Oxygen: red
        • Nitrogen: blue
        • Sulfur: yellow
        • Iron: yellow
  1. Advanced RasMol Usage:
The command line may also be used to perform more advanced commands. To find the commands, look in the RasMol manual under Help (PC) or  /Basic Instructions. Other helps, such as reference manuals and tutorials, are available on the Internet:



Swiss-PdbViewer (SPdbV) is an easy-to-use and powerful molecular modeling program. In addition to its many built in features, it is tightly linked to Swiss-Model (, an automated homology modeling server run by the Geneva Biomedical Research Center. For proteins of known sequence but unknown structure, SPdbV submits amino acid sequences to ExPASy to find homologous proteins, onto which a preliminary three-dimensional model may be built. Then SPdbV submits the alignment to ExPASy, where a final model is built and returned by e-mail.

Start the program
(Unless otherwise stated, "click" means a left mouse button click.)

Double-click on the Swiss-PdbViewer icon to start the program. Click anywhere on the startup banner to begin working.
Go to File > Open PDB file to locate and open a pdb file, such as 1cca.pdb. Click on OK; button on any dialog that appears. (You may accept default or change Rendering Attributes settings).

Obtaining helps
Each window has a small red "?" (question mark). Clicking the question mark will bring up help information about using that particular window. An alternative way is to consult the Swiss-PdbViewer "Help" menu, which has help items for each window. For detailed modeling instruction, do Help > Local Manual and your web browser will automatically load the User Guide

The SwissPdbViewer Windows
After the protein pdb file is loaded, SPdbV opens two windows: the Control Panel, and the display or graphics window. The Control Panel is used to select, label, and color residues. The graphics window and the tool buttons on it are used to view, manipulate, and measure the model. Only the active window with blue caption color responds to mouse or keyboard actions. The first click on an inactive window activates it, but does not cause any other change. Three other useful windows may be made visible from the "Display" menu.

Displayà Show Sequences Alignment

The narrow "Align" window appears below the graphics window, showing the amino-acid sequence of the protein in one-letter abbreviations

Display > Show Ramachandran Plot

This window could be used to judge the quality of a model, by detecting residues whose conformational angles lie outside allowed ranges. The Ramachandran Plot window may also be used to alter the backbone: directly modify the f /y angles of a residue by dragging the little cross to its new location. The rotation around either of the f or y axis during this operation may be constrained by holding down the "9" or "0" key while moving the cross. By default it is the C-terminal part of the protein that will move, as a little 'C' appeared just below the help icon (?). To move the N-terminal instead, click on the 'C' for its changing into a 'N'. To move only a part of the backbone (not the whole backbone up to the C-terminal), first break the backbone after the last amino-acid that will move. This is done with the appropriate item of the tool menu

Displayà Show Layer Infos

This table provides control of multiple protein models, Use it to choose which models are visible, which can move, and determine certain display features for each model.

Another two small icons
Below the first tool button (Window Attributes), there are two symbols, a globe (or protein) icon and paper icon. Click the paper icon to see the PDB file. Click the globe icon to switch to little protein icon. The globe icon indicates that the rotation takes place in absolute coordinates, while the protein icon indicates the rotation is around their centroid. Hence the first option allows you to rotate the molecule around any atom, providing that this atom has previously been centered (translated to the (0,0,0) coordinate). 

 Manipulate the model
1.     Click on the graphics window to make it active.
2.     Click the first tool button in the left to bring up the "Rendering attributes" dialog. These parameters could be adjusted for viewing convenience. (I.e. Adjusting "Slab depth" is very useful while investigating active site or when an electron density map is visible.
3.     The "Translate", "Zoom" and "Rotate" tool buttons are used to manipulate the protein model. Click to activate the button first, then drag the mouse around to see the effects (the mouse cursor appearance changes to match the active tool).
4.     Pressing "Insert" key or right clicking anywhere on the graphics window moves and scales the visible molecules to fit the view.

Select and Display the model
Under Control Panel:
  • Press "Enter" - Display only selected groups and hide others.
  • Press "+" on the numeric keypad - Add the selected groups to the view without hiding non-selected groups.
  • Right click column header - Check only the selected residues.
  • Right click on residue – Center the view on the residue, do not select it.
Under Select menu:
  • All - Select all residues of the current layer. Holding the "Shift" key to select all residues of all layers.
  • None - Deselect all residues of the current layer. Holding the "Shift" key to deselect all residues of all layers.
  • Inverse Selection - Simply inverses the selection. For example: for selecting all residues but basic ones, first select basic residues, then inverse the selection.
  • Extend to other layers - This is typically used after a structural alignment has been done. It allows selecting some residues in one layer, and automatically selecting their counterparts in other layers. It is kind of useful to compare active sites of several proteins.
  • Pick on screen – Select multiple residues directly form the screen. "Esc" ends the selection. To add the picked residues to the previous selection, hold the "Control" key down while invoking this command. Note: This command will only allow selecting residues of the current layer. This is especially useful when two residues of separate layers are exactly superposed, because only the residue of the current layer will be selected.
  • Group Kind - This submenu allows selecting residues by type (different type of amino acid, nucleotide, HETATM, solvent and S-S bonds).
  • Select Acidic amino acids - Select Asp and Glu.
  • Select Basic amino acids - Select Arg, Lys and His.
  • Select Polar amino acids - Select Asn, Gln, Ser, Thr and Tyr
  • Select non Polar amino acids - This will select Ala, Cys, Gly, Ile, Leu, Met, Phe, Pro, Trp and Val
  • Helices, Strands, Coils - Select all the residues in the corresponding secondary structure elements.
  • Visible Groups - Select the residues currently visible. In slab mode, only select groups within the view window.
  • Reconstructed amino acids - Select residues whose sidechain has been reconstructed. It should be noted that incomplete pdb files are completed upon loading.
  • Neighbors of selected aa - Extend a selection around a previous selection.
  • Groups Close to another chain - This is useful for investigating the residues at the interface of two chains. (I.e. examining how dimers or multimers are bound to each other.)
  • Groups Close to an other layer – Similar as above.
  • Accessible aa - Select residues in a certain surface accessibility.
  • Groups with same color as - This allows picking a residue on screen, and selecting all residues that have the same color. This is useful for changing groups color from one kind (I.e. red) to another (I.e. yellow).
  • aa identical to ref. - After a structural alignment has been done, invoke this command to select residues that are strictly conserved between the current layer and the reference protein (the first loaded).
  • aa similar to ref. – Similar as above, will select conserved residues. The PAM200 matrix will be used, and the minimum score needed to be considered similar can be modified in the "Alignment" Preferences. Decreasing this stringency value will increase the number of amino acids considered as similar.
  • non Trans aa - This will select residues whose w angle is below a certain value. Typically residues are trans (around 178 deg.) This lets you select distorted residues or look at cis residues.
  • aa with phi/psi out of core regions - This will select residues that lay outside of the "core" region (the region where most of the residue should lay).
  • aa with phi/psi out of allowed regions – Similar to preceding. Few residues (except Gly which lacks a sidechain) should lay outside of the allowed regions.

Under Display menu:
  • Show Control Panel - Bring the control Panel to the front.
  • Show Layer Infos - Bring the Layer Infos Window to the front. This window controls the display features of each layer (visible, movable, CA, H2O etc…).
  • Show EDM Window - Bring the Electron Density Map Window to the front. This lists the currently loaded electron density map, and controls how it is displayed (unit-cell, coarse contouring, sigma contouring value, color, dotted or plain lines). Holding the "Control" key brings up a more complete dialog.
  • Show Ramachandran - Show the Ramachandran plot of the currently selected amino acids.
  • Show Sequences Alignment - Show the Alignment window, which is useful when comparing multiple proteins that have been matched in 3D. It may aloso be used to select residues.
  • Show Text Window - Bring the Text Window to the front. The text window could contain a PDB file, an on-line help, or any other text files which have been opened with File > Open Text File.
  • Label Kind - This is used to select label display type. The default label is the group name that appears on the a carbon, but other options (atom names or atom type) are available.
  • Slab - When enabled, only residues between the two Z clipping planes are displayed. The default slab depth is 10 Å, but it may be changed in the "Rendering Attributes" dialog. Initially, the slab is centered on z=0, but could be moved by holding the "Shift" key and moving the mouse with the left key pressed. Note: The slab mode will display/undisplay an amino acid entirely as soon as its CA (C1_ for nucleotides) is in/out of the slab. This removes unlinked atoms and bonds from the display. However, this rule does not apply for HETATM groups.
  • View from – View the molecules from different angles.
  • Show CA trace only – Display the "backbone" structure. (lines connecting CAs)
  • Show Backbone Oxygen – Show or hide backbone oxygens.
  • Show Sidechains even when Backbone is hidden - When enabled, this menu allows the display of sidechains even when no check mark is present in the show column of the control Panel. This can be useful for certain kinds of final renderings with ribbon representation of the protein.
  • Show Dots surface - When checked, this menu allows the display of van der Wals surfaces. It supersedes the setting found in the "dot" column of the Control Panel. Because Dot surface can take a long time to compute, it is often helpful to temporarily undisplay them, modify the display, and then redisplay them without having to change the set of dotted residues.
  • Show Axis - When checked, the axis orientation of the first protein loaded will appear at the top left of the screen. It should be noted that it is different from the axis that can be displayed from the Layer Infos Window, which always appear at the (0,0,0) coordinate of each concerned layer.
  • Show H-bonds – This command is available after H-bonds have been computed.
  • Show H-bonds distances - Draw the distance between donor and acceptor at the middle of each H-bond.
  • Show only H-bonds from selection - Show H-bonds whose one pair belongs to the selected groups (groups appearing in red in the control panel).
  • Show only groups with visible H-bonds - Allows focusing on important things. For example: In order to display only groups that make H-bonds with an enzymatic cofactor (NAD, ATP...), click on the cofactor name in the control panel (it is now the only selected group), then select "show only H-bonds from selection", and then "show only groups with visible H-bonds", which will clean-up the view.
  • Render with Q3D - This will generate a solid image with Apple Quickdraw 3D™. Colors, lights, appearance and kind of renderer can be altered in the two appropriate preferences dialogs (Q3D rendering and Q3D light).

Use Swiss-PdbViewer "Preferences" menu

A default preferences file is created or altered each time the program exits. This file contains the exact configuration present at the time the program exits. Several different preference files may be used as "style sheets" for different modeling tasks.

Under Swiss-PdbViewer "Preferences" menu:
  • Modify last Prefs dialog - Display the last preference dialog that could be modified.
  • Open - Replace the current settings (Default.prf) with those stored in the alternate file.
  • Save - Saves the current settings in a file for future usage. Note that the current settings are always automatically saved in the "Default.prf" file when the user quits the program.
  • General - This dialog mainly allows the user to alter the behavior of the program at startup and when a file is loaded.
  • Loading Protein – Alter the protein loading attributes. For example, the protein could be loaded with: color by secondary structure; a solid ribbon displayed instead of the wireframe representation; superposition onto previously loaded proteins; and a structural alignment computed.
  • Real Time Display - In order to insure a "smooth" handling of real-time molecule displacements, a number of options aimed to reduce the CPU load while the molecule is moving are provided. If the number of lines needed to draw the display exceeds the maximum, the program will first attempt to draw the molecule without stereo view, then without hydrogens, and finally without sidechains. For extraordinarily large displays, the program can be configured to draw only one group out of n.
  • EDM - This dialog controls the display of electron density maps. The same map can be simultaneously contoured at two different sigma levels with different colors. For fast rendering, a coarse contouring along one or several of the unit cell axes may be used. The unit cell axis are colored in red for a, green for b and blue for c.

SwissPdbViewer File operation

Loading protein molecule: Select the "Open" item from the "File" menu, or select one of the recently opened proteins that appear at the bottom of the file menu, then the molecule will appear in the display window.

Adding molecules: Same as loading protein molecule.

Exporting molecules: Molecule may be saved in the exact orientation it appears on screen by choosing the "Save PDB" item of the "File" menu. All atoms of the current molecule (the current molecule is the one whose groups are listed in the control panel, and whose name appears in the Display Window title bar) are exported, even if they are not displayed. The screen image may be saved as a BMP file by choosing "Export Image". For a larger image, simply enlarge the Display Window Size before exporting the image.

Merging molecules: Fragments coming from different molecules may be merged to build a new entity. This is done by selecting in each layer the groups that will appear in a new layer, and then use the "Create Merged Layer" item of the Edit Menu. The "merged" molecule will appear in a new layer, which can be renamed using the "Rename Current Layer" item of the "Edit Menu".

Discarding molecules: Remove all molecules by choosing the "Close" item of the "File" menu. Remove the current molecule (the one whose groups are listed in the control panel) by hitting the "Delete" key