[Chimera-users] Defining Attribute Color for Surface Independent of Atoms
Chimera Folks, I have set up a file to define a series of colors based on functional measurements for some residues in a PDB file. I would like to color the ball and stick atoms according to element type and a semi-transparent surface according to the colors defined by my text file. It seems like these two things are tied together; that the surface can either be colored by the model, the atoms, or a specific color. Can I color it according to a Defined Attribute but leave the atoms as CPK coloring? Thanks, David
On Tuesday, January 25, 2005, at 10:14 AM, David Piper wrote:
I have set up a file to define a series of colors based on functional measurements for some residues in a PDB file. I would like to color the ball and stick atoms according to element type and a semi-transparent surface according to the colors defined by my text file. It seems like these two things are tied together; that the surface can either be colored by the model, the atoms, or a specific color. Can I color it according to a Defined Attribute but leave the atoms as CPK coloring?
Dear David, Yes, the surface can be colored separately from the atoms. If you already used Define Attribute to create your attribute, then just use the Colors section of Render by Attribute (Tools... Graphics... Render by Attribute). Uncheck the box to "Color atoms" and make sure the "Color surfaces" button is checked. The coloring will then be applied to just the surface. The manual page for Render by Attribute: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html You could do basically the same thing with the command "rangecolor" where putting ",s" right after the attribute name indicates that coloring should apply to the molecular surface. The manual page for rangecolor: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html Another way is to use Define Attribute to assign values directly to the atom attribute "surfaceColor" ("color" is the atom color, "surfaceColor" is the color of that atom's surface, and they don't have to be the same as each other). The last example file linked to the Define Attribute shows a similar approach. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ rescol.txt I hope this helps, Elaine --- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
This might be simpler, but in situations like these I just open the pdb file again, use one model say #0 for defining the colors on the atoms/bonds, and model #1 for defining colors on the surface. You can then turn the atoms/bonds display off for your surface (model #1). Elaine Meng wrote:
On Tuesday, January 25, 2005, at 10:14 AM, David Piper wrote:
I have set up a file to define a series of colors based on functional measurements for some residues in a PDB file. I would like to color the ball and stick atoms according to element type and a semi-transparent surface according to the colors defined by my text file. It seems like these two things are tied together; that the surface can either be colored by the model, the atoms, or a specific color. Can I color it according to a Defined Attribute but leave the atoms as CPK coloring?
Dear David, Yes, the surface can be colored separately from the atoms. If you already used Define Attribute to create your attribute, then just use the Colors section of Render by Attribute (Tools... Graphics... Render by Attribute). Uncheck the box to "Color atoms" and make sure the "Color surfaces" button is checked. The coloring will then be applied to just the surface.
The manual page for Render by Attribute: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html
You could do basically the same thing with the command "rangecolor" where putting ",s" right after the attribute name indicates that coloring should apply to the molecular surface.
The manual page for rangecolor: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html
Another way is to use Define Attribute to assign values directly to the atom attribute "surfaceColor" ("color" is the atom color, "surfaceColor" is the color of that atom's surface, and they don't have to be the same as each other). The last example file linked to the Define Attribute shows a similar approach.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ rescol.txt
I hope this helps, Elaine --- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
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participants (3)
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David Piper -
Elaine Meng -
Sabuj Pattanayek