[Chimera-users] PipesAndPlanks coloring not accurate

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 17 18:33:37 PST 2017

Hello Andrew,
You’re right that the Pipes-and-Planks model’s color can’t be changed after creation, and that that is inelegant.  Another limitation is that each secondary structure segment can only be a single color, so you can’t make a color boundary that falls in the middle of a pipe, plank, or coil segment.  Instead, as mentioned in the docs

…A “No Color" setting indicates that each pipe, plank, or stretch of coil should be colored using the residue color (ribbon color) of its first residue.”

I’m guessing that your input color boundary falls in the middle of one of those but it gets shifted in the result due to this limitation.  The within-Chimera solution is to make sure that the ribbon of the first (most N-terminal) residue of the coil in the initial structure is tan to make the whole coil segment tan, but I understand that’s not quite accurate either.

We definitely realize these limitations are pretty annoying and it has been remedied in our new program ChimeraX, in that helix cylinder representations are fully integrated with ribbons and the color can be different for each residue.  However, ChimeraX does not have “planks” per se, only strand ribbons that may be a bit wavy rather than straight (although they can have a rectangular cross-section).  It also does not have the arrow (cone) option on the cylinders.  However, if you wanted to try ChimeraX for this figure, there are some example images with helix-cylinder representations and corresponding ChimeraX command scripts (.cxc files) here:


The first one also has rectangular cross-section strand ribbons.  Just opening the .cxc file in ChimeraX will generate the figure except for the structure’s orientation, but you can use the mouse to rotate. Like Chimera, Chimera is free for noncommercial use and available for download, see website: <http://www.rbvi.ucsf.edu/chimerax/index.html>

Sorry about the limitations.  I hope this helps to clarify what’s going on, at least!
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 17, 2017, at 6:04 PM, Andrew Hagen <arhagen at lbl.gov> wrote:
> Hello,
> I have a protein model that I colored according to region:
> N-terminal domain (green), 
> a domain that I inserted (gray),
> and the flanking (GGS)2 linkers (tan). 
> When I apply PipesAndPlanks, the tan regions are changed to either green or gray, which is not desired (and apparently, the PipesAndPlanks' color cannot be changed once rendered). Is this a bug or am I doing something wrong?
> To add a little more detail, I manually Frankensteined this model together. At the genetic level, it's just a domain insertion, flanked by linkers, but in Chimera I did this by: 
> Opening my wt protein model (green), splitting the chain into two models at an internal site, generating GGSGGS linkers de novo in Chimera and joining these to the new models, and then finally joining those two fragments through a "bridge" of another model. There was lots of manual torsioning and minimizing using FoldIt in this process.
> I can imagine a work around is just to overlay two PipesAndPlanks renders and masking different regions, but this seems inelegant.
> Any assistance/advice is appreciated!
> --Andrew
> <Post_pipes.png><Pre_pipes.png><Frankenprotein.pdb>_______________________________________________
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