[Chimera-users] on preset interactive 1 color

Smith Liu smith_liu123 at 163.com
Sat Dec 12 07:02:05 PST 2015

Dear Elaine,
Suppose I have colored chain A a specific color, and I have shown A180 sidechain as sticks and balls. Is any routine way we show the sidechain N in blue and O in red?

At 2015-12-12 01:48:53, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
>Dear Smith,
>For a single multi-chain structure, the ribbons (interactive 1) preset just does the same thing as command “rainbow chain”.  It does not use color names. It just uses the rainbow across how ever many chains you have, starting with blue for the first chain and ending with red for the last one, and different colors for the ones in between depending on how many chains are in the structure. Details:
>In general, if you’re making a figure you should describe the colors as they look to you.  It doesn’t really matter if the color name in Chimera is “cornflower blue” … if it just looks like light blue to you, it will probably look that way to the readers of your paper, so you can just call it light blue.
>However, as the “interactive” suggests, this preset’s coloring is to help you distinguish the chains during interactive use, and it is usually not the best coloring to use for a figure.  For a figure, you might want to use a white background and black outlines, such as in publication preset 1, and change the chains to whatever colors you like.  
>You can color each chain by selecting it with the Select menu and using Actions…Color to color it.  You can get more colors by choosing Actions… Color… all options and checking “show all colors”.  Or you can just use commands, for example:
>color pink :.A
>color cornflower blue :.B
>… to color chains A and B.  Another place to see the color names:
>I hope this helps,
>Elaine C. Meng, Ph.D.                       
>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>Department of Pharmaceutical Chemistry
>University of California, San Francisco
>On Dec 10, 2015, at 10:24 PM, Smith Liu <smith_liu123 at 163.com> wrote:
>> Dear All,
>> If by chimera we select preset interactive 1 for a protein complex, each chain will take a different color. As for when we describe the corresponding colors in a paper we need to know the names of each color by the chimera preset interactive 1 function, and the colors by this function are usualy very close to each other, will you please introduce to me the color names colored by the function preset interactive 1?
>> Smith
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