Using MATLAB to analyze principal components obtained from a molecular dynamics simulation of a pro

If you have the output of the covariance matrix (CovMat) you can visualize it with imagesc(CovMat). If you want the cross correlation map (CCMap) you can obtain this with:
CCmap = zeros(length(CovMat)/3,length(CovMat)/3);
for i = 1:length(CCmap);
    for j = 1:length(CCmap);
        CCmap(i,j)= trace(CovMat(3*i-2:3*i,3*j-2:3*j))/(sqrt(trace(CovMat(3*i-2:3*i,3*i-2:3*i)))*sqrt(trace(CovMat(3*j-2:3*j,3*j-2:3*j))));
    end
end
imagesc(CCmap)

I'm not sure what  you mean by visualize the different eigenvectors. If you want to see the vectors plotted on the protein what I have used was NMWiz a plugin for VMD. Information here: http://www.csb.pitt.edu/ProDy/plugins/index.html