Joint Histogram Function for Ramachandran Plots

I am currently working on Ramachandran plots for the dihedral angles obtained from MD simulations. I have uploaded the data into Igor and developed a scatter plot of the psi and phi angles. However, I am unsure how to use the JointHistogram function to make the Ramachandran plots of psi vs phi. Is there something I need to calculate? I know once I use the function, I can Append a contour plot onto the scatter plot that I have created. I do not know how to proceed. I am attaching my scatter plot to this post. I am technically missing the color gradient for the densities (including a plot I made using python as a comparison). 

psi vs phi scatter Python Ramachandran plot

Hi,

To get a color scale, go to add annotate in the graph menu and select colorscale from the annotation type.  You may have to rearrange axis and others to make space for the color scale.

As far as the two graphs you are showing, they have the same basic form so I thing you have the basics ok.  One question would be the binning size you used.  The Igor plot seems a bit binary  with a fine texture as if each populated bin has a count of 1 and the others 0.  If you examine the values do they fall into meaningful ranges and values.  Look at the joint histogram in a table.  The other way is to use the joint histogram wave in a gizmo plot and use a 3D bar chart to see heights.

If that comes out to your satisfaction, then I would look to modify image to see the color range that is being used makes sense.

Andy

In reply to by hegedus

I cannot do the color scale without having the values I need, and I am having trouble with knowing the numbers I need for the joint histogram table. I put int #include <Bivariate Histogram 2> in the procedure window, but I know I need a code that applies it for the density plot. I do not know what code it is. I tried this code that I found on the forum, but it does not work and says this error message for the first line: expected wave name, variable, or operation

wave P1_phi_angels, P1_psi
make/D/O/N=(50,75) ramahist
JointHistogram(P1_phi_angels, P1_psi, ramahist)
Display/N=ramahist; AppendImage ramahist
ModifyImage ramahist ctab= {*,*,Spectrum,0}
ColorScale/E/C/N=Density
AppendtoTable ramahist
end

 

Assuming that you have Igor 7 or newer the following function gives you a basic density plot based on the JointHistogram operation:

function BasicDensityPlot(w1, w2)
    wave w1, w2
   
    JointHistogram w1, w2
    wave M_JointHistogram
    NewImage M_JointHistogram
    ModifyImage M_JointHistogram ctab= {*,*,Spectrum,0}
end

 

Thank you for the help! I was able to successfully complete the plots. Turns out I only needed this part of the code:

JointHistogram w1, w2
wave M_JointHistogram
NewImage M_JointHistogram
ModifyImage M_JointHistogram ctab= {*,*,Spectrum,0}

 

Ramachandran Plot