COMBOSA3D - Coloring Of Molecules Based On Sequence
Alignment scroll down for help
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.
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window
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. For more information on experimentally determined
molecular structures and PDB ID numbers see the Protein
Data Bank.
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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.
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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. You can click
on residues in the solved sequence to label the corresponding residues
on the molecule.
-
Important: confirm that the solved structure is in proper register
with the solved sequence in the reference alignment. To do this, click
on characters in the solved sequence (in the reference alignment) to label
residues on the molecule. If the amino acid names 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.
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Alternatively, if your computer cannot handle zipped files, you can save
the individual files by right clicking (click and hold with Macintosh)
on the following links (once these files are saved in the same directory
load index_b.html into your Web browser):
To use COMBOSA3D you must have the Chime
plugin version 2.0 or higher (© MDL Information Systems, Inc.)
installed on your machine.
Resizing this window may cause some formatting options to
be restored to their defaults. If resizing causes molecule clipping, refresh
or reload the page. Try clicking BACK if formatting is lost.
Multiple copies of this page should not be run simultaneously.
Check
for Web browser compatibility.
Thanks to Eric Martz for helpful suggestions.
COMBOSA3D copyright
© 2000 Paul
Stothard