COMBOSA3D - Coloring Of Molecules Based On Sequence Alignment scroll down for more info

COMBOSA3D is used to color a three-dimensional representation of a protein according to the results of a sequence alignment. The program accepts a group of pre-aligned sequences in FASTA format (one of the sequences must have a solved three-dimensional structure), and it uses the alignment information to highlight conserved residues on the molecule. Three-dimensional structures are shown using the Chime2.0 plugin, currently available for Windows 95/98/NT and Macintosh from MDL Information Systems, Inc. You can use the program without the Chime plugin, and instead use RasMol to view and color a molecule (see the instructions below).

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How to use COMBOSA3D with the Chime plugin:
  1. In the Molecule Control pane enter the PDB ID number of the solved molecule you want to color and click Load. For more information on experimentally determined molecular structures and PDB ID numbers see the Protein Data Bank.
  2. In the Sequence pane enter the pre-aligned sequences you want to use for coloring the loaded molecule (sequence alignments in FASTA format can be generated using the BCM Search Launcher). The solved sequence (the sequence corresponding to the loaded molecule) must appear in the second text area. You can also include the solved sequence in the first text area if you want the identity and similarity calculations to include this sequence.
  3. In the Sequence pane choose the colors you want to use to highlight conserved regions of the molecule.
  4. In the Sequence pane click Color Molecule to apply the color scheme to the loaded molecule.
  5. In the Sequence pane click Show Alignment to generate a reference alignment that displays how the color scheme was generated.
  6. Important: confirm that the solved structure is in proper register with the solved sequence in the reference alignment. To do this, select Residue Labels from the Toggle list in the Molecule Control pane, and click On. You may find the labels easier to read if you select Ribbons from the Display mode list and click Send. If the amino acid names and numbers appearing on the molecule don't match the solved sequence in the reference alignment the sequences are out of register, or the PDB file contains residues that are different from the solved sequence you entered. You can place the solved sequence into proper register with the three-dimensional structure by entering a new starting position for the solved sequence (in the Sequence pane), and repeating steps 4 and 5.
  7. Use controls in the Molecule Control pane to adjust the appearance of the molecule and to send a picture of the molecule to the Clipboard.
How to use COMBOSA3D without the Chime plugin:
  1. In the Sequence pane enter the pre-aligned sequences you want to use for coloring the loaded molecule (sequence alignments in FASTA format can be generated using the BCM Search Launcher). The solved sequence (the sequence corresponding to the molecule you plan to color) must appear in the second text area. You can also include the solved sequence in the first text area if you want the identity and similarity calculations to include this sequence.
  2. In the Sequence pane choose the colors you want to use to highlight conserved regions of the molecule.
  3. In the Sequence pane click Show Alignment to generate a reference alignment that displays how the color scheme was generated.
  4. In the Sequence pane click Color Molecule to generate a RasMol script. The script will appear in the Script text area, in the Molecule Control pane.
  5. Copy the RasMol script and follow the instructions for using RasMol.
  6. Important: confirm that the solved structure is in proper register with the solved sequence in the reference alignment. Using RasMol, label residues in the molecule and confirm that the residue names and numbers match those in the solved sequence in the reference alignment. If they don't match, the sequences are out of register, or the PDB file contains residues that are different from the solved sequence you entered. You can place the solved sequence into proper register with the three-dimensional structure by entering a new starting position for the solved sequence (in the Sequence pane), and repeating steps 3 and 4.

Downloading COMBOSA3D:
  • Multiple copies of this page should not be run simultaneously.
  • Thanks to Eric Martz (University of Massachusetts, Amherst) for helpful suggestions.

  • COMBOSA3D copyright © 2000 Paul Stothard