[Chimera-users] rainbow with atom-spec of a portion of a chain

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 13 16:10:24 PDT 2017


Hi Micah,
Ah yes, you’ve run into a limitation mentioned in
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rainbow.html>

"The coloring cannot be limited to a subset of the polymer chains in a model or to a subset of the residues in a chain…”

A somewhat laborious, inelegant workaround is to open two copies of the structure and from whichever one seems to “win” the display (can tell by model color), delete the non-rainbow portion and then rainbow that copy. However, due to the ribbon path interpolation, if you are showing ribbon the ends stick out from the full copy.  You would need to further fudge things by including a 3-4 extra residues of overhang on both ends of the truncated copy and then undisplaying the ribbon for those overhangs.

Then you don’t get the full rainbow range (the reddest and bluest parts are hidden) but it might be good enough for your purposes. 

Example:

open 2gbp
open 2gbp
… still looks tan, so the first copy #0 is “winning” the display, delete from that one
delete #0 & ~ :30-106
rainbow #0
~ribb #0:30-33,103-106
modelcol white #1

… gives (at least for me) the appearance in the attached image.  If you had the problem of the other model showing through, you could use Ribbon Style Editor to ensure that the ribbon of the rainbow copy is slightly fatter and wider than the other one.

Sorry I didn’t have a nicer answer, but I hope this helps.
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco



> On Jul 13, 2017, at 10:34 AM, Cheng, Micah <Micah.Cheng at fccc.edu> wrote:
> 
> I was trying to rainbow a subset of a chain using the rainbow command and the atom-spec:
> rainbow #0:34-102.a
>  
> However when run, the entire chain A was colored with rainbow instead just residues 34-102
> running the color command with the same atom-spec:
> color #FFFFFF #0:34-102.a
> produced the predicted result of only residues 34-102 being colored white
> Is there a command to rainbow only part of the chain or are there any workarounds to being able to rainbow only a selected portion of a chain?
>  
> Thanks in advance
> Micah
> 

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