Dear Wee Zhang, Chimera does not have a "spring" style for bonds.

However, you can create pseudobonds (which are like fake bonds) between pairs of atoms and then show the pseudobonds in a "spring" style.

(1) If you open your structure and it already has bonds you would need to delete the normal bonds, example:

open 1gcn display ~ribbon ~bond

Then you would have a bunch of dots that are the atoms. There are several different ways to add pseudobonds.

(2a) One way is to create a text file specifying the pairs of atoms between which you want to add pseudobonds and then use the Pseudobond Reader tool. Details of the file and the tool here: https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html

(2b) Another way is to make distance measurements between all the pairs of atoms. This can be done with the "distance" command, for example

distance :1@ca :2@ca

...or with Ctrl-click on one atom, Shift-Ctrl-doubleclick on the second atom and then choosing "Show Distance" from the popup menu.

https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html

(3) Then you would need to change all the pseudobonds to "spring" style, change color if you like, and if they are distance measurements, hide the distance label. For example, commands

setattr p drawMode 2 setattr p color magenta setattr p label ''

(the last part is two single quote ' characters without space between them, meaning the label should be nothing)

https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.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 10, 2023, at 1:33 PM, Wee Zhang via Chimera-users chimera-users@cgl.ucsf.edu wrote:

Dear RBVI Team,

I hope you are doing well. I am writing to inquire about the capabilities of the UCSF Chimera software in visualizing bond atoms in a spring mode, similar to the exemplary images I have enclosed for reference. I have been using UCSF Chimera for various molecular visualization and analysis tasks, and I am particularly interested in exploring this feature for my research and projects.

The visualizations I am referring to are those that effectively represent covalent bonds as springs connecting atoms in a molecular structure. These spring-like representations can provide valuable insights into the flexibility and dynamics of molecules, which are crucial aspects of my research in materials science.

I have attached images that illustrate the visualizations I want to achieve with UCSF Chimera for your reference. These images serve as excellent examples of dynamic and informative representations that I believe could greatly enhance my research.

I would appreciate it if you could provide information on whether UCSF Chimera can generate bond atom visualizations in a spring mode, and if so, any guidance on how to achieve this would be beneficial. Additionally, if any specific plugins or settings are required to create such visualizations, please let me know.

Furthermore, if any workshops, tutorials, or resources can assist me in mastering this feature, I would be eager to participate in or access them.

Thank you in advance for your time and assistance. I look forward to hearing from you regarding the feasibility of incorporating the spring mode bond atom visualization into UCSF Chimera and any guidance you can provide on achieving this.

Please feel free to contact me via email at [your email address] or by phone at [your phone number] if you require additional information or clarification.

Sincerely, <WhatsApp Image 2023-09-09 at 12.00.35.jpg><WhatsApp Image 2023-09-09 at 12.00.36.jpg>