[Chimera-users] Coloring model represented as PipesAndPlanks

[Elaine Meng]

Hi Ibrahim,
As far as I know the Pipes and Planks have only been whatever colors  
are shown in the PipesAndPlanks dialog, and these colors can be  
different than the protein structure.  It doesn't matter whether the  
model number is the same or different as the protein structure for  
purposes of coloring.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pipesandplanks/pipesandplanks.html 
 >

Is it possible you were using Axes before?  With Axes/Planes (now Axes/ 
Planes/Centroids in version 1.5), each helix can be shown as a  
cylinder, and each cylinder can be colored however you like.  This  
tool does not make "planks" for beta-strands, however.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes 
 >

With molmap you can specify the new map's model number, for example:

molmap ligand 5.0 model 4

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>

The model number doesn't affect coloring.  The reason one might want  
models to have the same number is that it prevents you from moving  
them separately (prevents decoupling their positions/orientations).
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


On Apr 1, 2010, at 7:44 AM, Ibrahim Moustafa wrote:

> Dear Chimera team,
>   I have a problem with coloring different regions of the protein  
> presented as PipesAndPlanks. I know I can change the colors of the  
> SS elements from the menu of PipesAndPlanks.
> But, this is not what I want: I want to color different regions of  
> the protein with different colors and not to be limited with the  
> colors given to the SS.
>
>   Before, I had no problem in doing so. I think this problem  
> appeared in the recent updates.
> Something I noticed and could be related is that to change the  
> presentation from the default chimera to PipesAndPlanks the new  
> presentation assigned the same model# as the original model. I  
> think, in previous versions the new presentation used to be given a  
> new model#. Similarly, if I want to create a map for the model using  
> (molmap) it is given the same model # rather than a new model# as  
> used to be.
>
>  I run Chimera version 1.4.1 (build 30282) on a Mac OSX 10.4 (PPC).
>  Thanks for help.
>  Ibrahim