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:
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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.
-
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.
-
In the Sequence pane choose the colors you want to use to highlight
conserved regions of the molecule.
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In the Sequence pane click Color Molecule to apply the color
scheme to the loaded molecule.
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In the Sequence pane click Show Alignment to generate a reference
alignment that displays how the color scheme was generated.
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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.
-
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:
-
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.
-
In the Sequence pane choose the colors you want to use to highlight
conserved regions of the molecule.
-
In the Sequence pane click Show Alignment to generate a reference
alignment that displays how the color scheme was generated.
-
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.
-
Copy the RasMol script and follow the instructions
for using RasMol.
-
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:
-
Download COMBOSA3D (combosa3d.zip).
Once you have unzipped the files, load index.html into your Web browser.
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