Coloring model represented as PipesAndPlanks
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 -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927
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/pipe...
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/struc...
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
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 Pymol. Thanks for the explanation. Ibrahim On 4/1/10 1:14 PM, "Elaine Meng" <meng@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/pipe... 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/struc... 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
participants (2)
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Elaine Meng -
Ibrahim Moustafa