Hi Trina,
I'm forwarding this to the chimera-dev list to give the "Ramachandran plot guy" (Conrad Huang) a chance to answer.  I think he's recently done many of the same things for a custom script so he's better suited for answering...

--Eric

Begin forwarded message:

From: Trina Manalo <trinamanalo_2014@depauw.edu>
Date: June 19, 2012 7:56:53 AM PDT
To: pett@cgl.ucsf.edu
Subject: Question about coloring the points on a Ramachandran plot

Hi Eric,

I had emailed you about the animated Ramachandran plots, which I have gotten to work. I have a new question to ask you concerning the points of the plot. 

I've tried coloring the plots by opening Chimera as an administrator and going to IDLE. Then I tried editing the file labeled "_init_" under the "Ramachandran" folder that comes with the program when it is installed.  In the file, under "def _displayData(self)" I tried to do 2 things: 

1. Change the non-selected residue points to be transparent, so that only the outlines of the non-selected residue points are visible. I want to do this so that the selected residue point is visible when it is behind a lot of points. I got it to be somewhat successful, however, only half of the points turn out this way. The other half turned out to be blacked out and I'm not sure why. 

2. Get rid of the non-selected residue points all together so that the only point I see is the residue point that I am interested in following. I tried adding the phrase "marker='None' " in the "ax.scatter" line, but that didn't work.

I'd greatly appreciate your help.

Thanks,
Trina