Fwd: Question about coloring the points on a Ramachandran plot
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
Below are the changes I made to make unselected points be drawn as outlines while selected points are filled. (This should be the same as your method 1, but I do not see any artifacts or strangeness like half the points being blacked out.) There is still the issue of the order in which points are drawn (points drawn earlier will be obscured by points drawn later). There is only a static list of points in the Ramachandran tool, so selected points that appear earlier in the list may be obscured by the outlines of unselected points that appear later in the list. One way to get around this is to reorder your list so that selected points appear at the end. Another possibility is to draw in two passes, first unselected then selected. I know the reordering method works because I've used it in another application; the two-pass method _should_ work but I've not tested it. Please let me know if my code or explanation does not work as expected. Conrad =================================================================== --- __init__.py (revision 36720) +++ __init__.py (working copy) @@ -53,13 +53,16 @@ MPLDialog.fillInUI(self, f) def _displayData(self): - colors = ['b'] * len(self.phi) + edgecolors = ['b'] * len(self.phi) + facecolors = ['none'] * len(self.phi) for n in self.selectedIndices: - colors[n] = 'r' + edgecolors[n] = 'r' + facecolors[n] = 'r' ax = self.subplot ax.clear() self._showRegion(ax) - ax.scatter(self.phi, self.psi, c=colors, picker=True) + ax.scatter(self.phi, self.psi, facecolors=facecolors, + edgecolors=edgecolors, picker=True) ax.set_xlabel("phi") ax.set_xlim(-180, 180) ax.set_xticks(range(-180, 181, 60)) On 6/19/12 10:52 AM, Eric Pettersen wrote:
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 <mailto:trinamanalo_2014@depauw.edu>> *Date: *June 19, 2012 7:56:53 AM PDT *To: *pett@cgl.ucsf.edu <mailto: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
_______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
participants (2)
-
Conrad Huang -
Eric Pettersen