
Hi Chimera Team, is it possible to color the active site of an enzyme let's say green after the coulombic coloring, without losing the last-mentioned? The coulombic coloring disappears when I try to color specific positions in the structure to green. Thanks in advance Sebastian

Hi Sebastian, Short answer is no, custom coloring (such as Coulombic) is either all or none for a given surface. However, one possible workaround is to open two copies of the structure, surface both copies, show Coulombic coloring on one surface and green (or whatever non-Coulombic coloring you want, possibly multiple colors) on the other. Then unsurf (~surf) the set of atoms you *don't* want to show Coulombic coloring for in the Coulombic copy and the other colors should show through. This presumes the Coulombic-colored surface "wins" display when two surfaces are shown in exactly the same place. It worked in my test, but it is possible you might have to try Coulombic-coloring the second copy instead of the first copy. I tried this and it looked reasonable. It might not look that good depending on the specific geometry of the surface. I also tried unsurfacing the complementary set of atoms in the other copy, but that looked terrible because there were gaps. 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 Nov 20, 2012, at 7:19 AM, Mock, Sebastian wrote:
Hi Chimera Team, is it possible to color the active site of an enzyme let’s say green after the coulombic coloring, without losing the last-mentioned? The coulombic coloring disappears when I try to color specific positions in the structure to green. Thanks in advance Sebastian

On Nov 20, 2012, at 7:19 AM, Mock, Sebastian wrote:
Hi Chimera Team,
is it possible to color the active site of an enzyme let’s say green after the coulombic coloring, without losing the last-mentioned? The coulombic coloring disappears when I try to color specific positions in the structure to green.
Hi Sebastian, Just in case you mean that you are trying to color atoms and the surface is also changing, you need to restrict the coloring to just atoms. If you are using the menus, use the "all options..." entry in the Color menu, which will allow you to restrict the coloring to just atoms/bonds. If you are using the color command append ",a" to the color name to restrict the coloring to just atoms/bonds, e.g. "color green,a :148". Of course, maybe the simplest thing is to color your structure first and then compute the coulombic coloring of the surface. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (3)
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Elaine Meng
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Eric Pettersen
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Mock, Sebastian