[Chimera-users] Coloring higher ordered structures

Tom Goddard goddard at sonic.net
Wed Oct 18 13:30:45 PDT 2017


Hi Frances,

  You can just ctrl-click on individual protein surfaces in the 3iyu capsid and color them with the color button in the Multiscale Models window (image attached).  This didn’t require splitting into chains, I just pressed Make Models in the Multiscale Models window, used mouse selection and the “Copies” button to extend the all copies I selected with mouse to all copies of the same chain.

  The Color Zone tool (menu Tools / Volume Data / Color Zone) can allow you to color patches of the surface specific colors.  But maybe if you are showing a zoomed in view of one capsomere you would use a solvent excluded surface (menu Actions / Surface / Show) instead of the multiscale surface to get more detail, and you can color the SES surface to match the atom colors.

	Tom


> On Oct 18, 2017, at 11:00 AM, Frances Shepherd <sheph085 at umn.edu> wrote:
> 
> Hello,
> 
> I’m working with a rotavirus capsid structure and I’d like to highlight individual residues on it if possible.  I’m using PDB #3IYU which I split into individual chains, and used the multiscale model function to create the capsid structure.  I’m able to color different surfaces, but it applies the color to each spot where the chain is on the entire capsid, rather than just one subunit.  I’d like to recreate the kind of figure from a paper by Zeller et al (2012), attached below.  Additionally, is it possible to color individual residues on a capsid structure? 
> 
> Thanks in advance!
> -Frances Shepherd
> <Screen Shot 2017-10-18 at 12.58.29 PM.png>
> 
> 
> 
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