[Chimera-users] TER Cards and Rainbow Colors

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 31 14:13:01 PST 2007

Hi Albion,
If you just want to undisplay the dashed lines signifying chain  
breaks but still have Chimera understand that the parts belong to the  
same chain, remove the TER cards and use the command


see http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/longbond.html

In older versions of Chimera it was "longbond" (without the tilde),  
but we decided it made more sense for ~longbond to undisplay these  
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 31, 2007, at 2:04 PM, Albion Baucom wrote:

> Is there any way to introduce TER records between breaks in a chain,
> and still have N->C coloring continuous through a single chain?
> I have for instance a structure with missing loops that were not
> observed in density. Therefore there are breaks in the main chain.
> This is a very common occurrence. To prevent spuriously long bonds I
> have introduced TER records between the breaks. Then when I apply
> rainbow coloring from N->C terminus I get the spectral coloring
> between TER records rather than from the beginning of the chain to
> the end.
> I tried the card BREAK, but evidently that is not interpreted by
> Chimera. Coloring by chain, or by model in the Rainbow panel does not
> produce the desired effect.
> Thanks
> Albion
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