How do we show the disulfide bond in ChimeraX? We refined two structures from the same cryoEM dataset. One structure shows this specific disulfide bond directly in ChimeraX. The other does not show the disulfide bond. How can we force it to show?
[cid:image002.png@01D9F29A.0E940F90] From: Zhang, Miao zhang@chapman.edu Date: Thursday, September 28, 2023 at 10:53 PM To: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: Coloring carbons to match cartoon How can I change the size of spheres? Two of them look too close, when shown with spheres. [cid:image001.png@01D9F25E.99BA47B0]
From: Elaine Meng meng@cgl.ucsf.edu Date: Tuesday, August 22, 2023 at 7:59 AM To: Zhang, Miao zhang@chapman.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Coloring carbons to match cartoon External Message
[External Message]
Dear Miao Zhang, If the cartoons are the model color, the easy way to keep the carbon atoms the same color is to avoid using "color byelement" and instead use "color byhet" which will color only the non-carbon atoms.
But if it is too late for that and too late for undo, yes, you can color just the carbon atoms any color you want. I don't know how you colored the cartoons but you would need to know their color so you can use the same one. If the cartoons are "sky blue," then you could color carbon atoms the same way, for example, command:
color C sky blue target a
The "C" is the element symbol for carbon.
If you don't know what color the cartoons are exactly (don't know name of color) you can try selecting part of the cartoon with Ctrl-click and then using the Selection Inspector tool (click green magnifing glass icon on top bar). In Selection Inspector, change from Inspect: Atoms to Inspect: Residues, which will then include "cartoon color" as a square. Click the square to open the system color editor showing that color. Usually the system color editor will include some way of seeing the hex code, in this case #87CEEB, which could also be used in a command:
color C #87CEEB target a
You can color cartoons and atoms at the same time with "target ac":
color C orange red target ac
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 21, 2023, at 9:37 PM, Zhang, Miao via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thanks so much. That worked. Another question. When colored by elements, the color of carbons in side chains is different from the cartoons. Any chance I can change the color of carbons to the same color as the cartoons. <image001.png>
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