Dear UCSF ChimeraX Team,
I am a big fan of your program and I have been greatly impressed with its capabilities. I want to express my deep appreciation for the "soft" visualization option provided in ChimeraX - the aesthetics truly appeal to me.
I've been utilizing ChimeraX to visualize my chromatin structure data. While I'm aware this might not be one of the intended uses, when I simulated the 3D structure of chromatin as a protein's cif file, the result looked fantastic.
Now I've encountered a challenge and I am hopeful that you might be able to provide some guidance. I am looking to represent gene expression as the size of the spheres in my chromatin structure, all in one figure. I am aware that Chimera has a method using "vdwdefine", essentially using the size of the B-factor to represent the atomic radius. Could you guide me on how to achieve this in ChimeraX?
Furthermore, if I want to include multiple columns similar to the B-factor, how can I add them to the cif? Using the "defattr" command feels a bit cumbersome. It would be very convenient if I could pack a lot of dimensional information (such as the gene density of this chromatin segment, CG content, chromatin opening degree, etc.) into a single cif file.
Do you have any suggestions or strategies on how to achieve these somewhat unconventional functionalities? Your assistance would be greatly appreciated.
Thank you for your attention and I look forward to hearing from you soon.
Best Regards,
Zhiyuan Liu
