MATLAB: How to change the properties of the atoms in a MOLVIEWER figure in Bioinformatics Toolbox 3.3 (R2009a)

.pdb3-d3dbankBioinformatics Toolboxdatadatabasemoleculeproteinstructure

I want to change the color and ambient properties of atoms in my molecule that I display with MOLVIEWER function.
I can’t use handle graphics to access the atoms and change their properties.

Best Answer

You will need to use the “Jmol Script Console” to change the appearance of the atoms in the molecule. For example, to change the color to green and ambient to 100 for oxygen:
pdbstruct = getpdb('1vqx');
molviewer(pdbstruct)
Then, go to “Tools -> Scripting Console” to open the “Jmol Script Console”, and execute the following commands:
$ select *.O
285 atoms selected
Script completed
$ color green
Script completed
   set ambient 100
ambientPercent = 100
Script completed
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