Dear Miao Zhang,
(1) showing disulfide bond. ChimeraX shows the bond if it is described in your input data, but doesn't automatically add more bonds. So the data file that shows the bond must already have a LINK or CONECT for that bond, whereas the other file that does not have the bond information. However, you can add the bond yourself, for example, using the command:
bond :cys@sg reasonable true
... if the distance is judged reasonable for the bond. This solution was mentioned on the chimera-users list if you want to see a specific example: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/thread/D2GBE5UEIU2XL4HEGW4TSPOPN765PKMQ/
(2) you can change the VDW radius of atom(s) in several ways, such as with the "size" command or using the Selection Inspector. Example commands using potassium channel:
open 1bl8 sel K
... if you open the Selection Inspector (menu Actions... Inspect, or click green magnifying glass icon) you can see the current radius is 1.370. You can change the radius by changing the number in the Selection Inspector, or using the "size" command, for example:
size sel atomRadius 1.2
https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 29, 2023, at 5:59 AM, Zhang, Miao via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
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?
<image002.png> 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. <image001.png>