Thank you for the prompt response. Unfortunately, I cannot open my XYZ file on Chimera. The attached file is my XYZ, and I would like to know if you are able to look it over. I investigated the source you provided for a standard XYZ format but perhaps you can give me more insight into why my XYZ file will not open.

NSU Security WARNING: This is an external email. Do not click links or open attachments unless you recognize the sender and know that the content is safe.

Hi Rade,

If ORCA writes XYZ files in "standard" XYZ format as described here: https://en.wikipedia.org/wiki/XYZ_file_format then Chimera should be able to read them as a trajectory (as described here: https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/movie/framemovie.html).

When you say "bond interactions", do you mean that bonds break and form over the course of the trajectory? Chimera can handle that, but it requires some arcane magic to turn that on -- I can describe the necessary steps if you need that capability.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

On Mar 8, 2021, at 1:25 PM, Rade Jibawi Rivera <rj687@mynsu.nova.edu> wrote:

Hello,

I am a student from Nova Southeastern University, and I am conducting research where I am interested in utilizing your software "Chimera" for visualization of molecular dynamics. My concern is if your software will be able to create a movie of bond interactions with multiple time frames using ORCA XYZ output files. I would greatly appreciate it if you can give in some input. I hope to hear from you. Thank you for your time and consideration.

Best regards,
Rade Jibawi Rivera

_______________________________________________
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu
Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users