[Chimera-users] Coloring model represented as PipesAndPlanks

Ibrahim Moustafa I.moustafa at psu.edu
Thu Apr 1 11:12:36 PDT 2010

Thanks Elaine,

  You are right. I got confused with which software was used to make the
figure in the way I asked about. I remembered now, for that figure I used

   Thanks for the explanation.


On 4/1/10 1:14 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

> 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/pipes
> andplanks.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/struct
> uremeas.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

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