| Bioinformatics Toolbox | |
Plot 3D protein structure
pdbplot(PDBid, 'PropertyName', PropertyValue ...)
pdbplot(..., 'Plotmode', PlotmodeValue)
pdbplot(..., 'Colormode', ColormodeValue)
pdbplot(..., 'Showlabel', ShowlabelValue)
FigureHandle = pdbplot(...)
| PDBid | PDBID can also be the name of a PDB structure or a file containing a PDB structure. |
| Plotmode | Property to select display backbone and side chains. Enter either 'backbone' or 'mainchain'. The default value is 'backbone' for the alpha carbon backbone. |
| Colormode | Property to select the color of atoms or folding patters. Enter 'atom', 'chain', or 'secondary'. The default is 'chain'. |
pdbplot(PDBid, 'PropertyName', PropertyValue ...) retrieves 3D information from the web for a protein (PDBid), and plots the backbone structure. Information for the protein is in the Protein Data Bank (PDB) database.
pdbplot(..., 'Plotmode', PlotmodeValue) selects a plot with only the alpha-carbon backbone or a plot with amino acid side-chains.
pdbplot(..., 'Colormode', ColormodeValue) selects the colors for a plot.
If Colormode is 'atom' and Plotmode is 'mainchain', atoms and connections are colored green for carbon, blue for nitrogen, and red for oxygen.
The Colormode is "chain', the entire structure is one color.
If Colormode is 'secondary', alpha helix patterns are colored yellow, sheets are blue, turns are gray and, non alpha helix are cyan.
pdbplot(..., 'Showlabel', ShowlabelValue) when Showlabel is true, displays the labels that represent each amino acid name and sequence number in the protein. The default is false.
FigureHandle = pdbplot(...) returns the handle for the PDB plot figure.
For more on viewing PDB molecules in MATLAB, see the molecule viewer in MATLAB Central
www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=808
Plot the 3D backbone structure for the protein Insulin-Like-Growth-Factor-1. The identification number for this protein in the PDB database is 1B9G.
1. In the MATLAB Command Window, type
pdbplot('1B9G')A figure window opens with the 3D structure for this protein. The figure title displays the identification number PDB Plot – 1B9G while the bottom of the figure shows the protein title or compound name Title: INSULIN-LIKE-GROWTH-FACTOR-1.
3. Rotate, translate, and zoom the structure with the MATLAB camera toolbar.
4. From File menu, select
Save to Figure file — Saves the plot to a MATLAB figure file
Print - Prints the plot
Close - Closes the current PDB plot figure window
Close All - Closes all the opened PDB plot figure windows
5. Select the different view options from the View menu or navigation tool on the right side of the figure.
Select an Plot option button:
Backbone - Plots c- alpha trace
Main Chain - Plots main chain
Select a Color check box:
Atoms - Color atoms based on predefined color code: Red = oxygen, Green = carbon, Blue = nitrogen
Secondary - Color secondary structures based on predefined color code: yellow = a-helix, blue = beta-strand, gray = turn, cyan = helix (non-alpha), green = all other structures
Select the Show check box:
Labels - Show amino acid sequence labels
6. From the Help menu, Help or Demos for Bioinformatics toolbox.
Bioinformatics Toolbox functions getpdb, pdbdistplot, pdbread, proteinplot, ramachandran
| | pdbdistplot | pdbread | |
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