[Chimera-users] pipes and planks

Elaine Meng meng at cgl.ucsf.edu
Fri Dec 2 16:41:23 PST 2016

Hi Kyle,
Just to clarify, to automatically pick up the ribbon color of the first residue, the color well(s) for Helix color etc. in the PipesAnd Planks dialog have to be set to “No color”, which is one of the options available in the Color Editor dialog that appears when you click a color well in Chimera.

On Dec 2, 2016, at 4:34 PM, Kyle Morris <kylelmorris at berkeley.edu> wrote:

> Hi Elaine,
> Thanks for this, very helpful! I hadn’t realised that pipes picks up the color from the original model and had been forcing it with helixColor. Can work around using this knowledge.
> ChimeraX looks like it’s going to be awesome.
> Thanks,
> Kyle
>> On 2 Dec 2016, at 16:07, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> Hi Kyle,
>> Unfortunately once it’s made, it’s made.  Instead you have to get the coloring you want on the original model, and then recreate the pipes (& planks). Each whole pipe would be the same color, though, taken from the ribbon color of the first residue in that helix; it is not divided into independently colorable per-residue segments. The new pipes model should overwrite the existing pipes model, but f you seem to be getting duplicate models, extras can be closed using the Model Panel (under Favorites in the menu). 
>> You could try to “highlight” a position by also displaying the atomic structure CA atom of that residue as a ball or sphere, but I don’t know how well that would meet your needs, sorry.
>> In our next-gen program ChimeraX, not yet publicly available but will be soon (as early development, not a finished product), 
>> <http://www.rbvi.ucsf.edu/chimerax/>
>> ...there are helix “tubes” (like cylinders but curved) that are better integrated with the atomic model and cartoon ribbons, and can be recolored even in per-residue segments after they are shown.  Example image with leucine segments in red attached below.
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> <tube.png>
>> On Dec 2, 2016, at 3:40 PM, Kyle Morris <kylelmorris at berkeley.edu> wrote:
>>> Dear Chimera dev,
>>> I am using the pipes representation. In this case is it still possible to color/highlight a segment by residue number? Using the normal commands when displaying pipes doesn’t update the color, only on the original model.
>>> Thanks for your help!
>>> Best wishes,
>>> Kyle
>>> scription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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