[Chimera-users] ORCA XYZ FILES

Rade Jibawi Rivera rj687 at mynsu.nova.edu
Wed Mar 10 13:46:38 PST 2021

Greetings Eric,

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.

Additionally, can you further explain how I would create the simulation/movie created from OCRA?

I look forward to hearing from you soon. Have a great day!

Best regards,
Rade Jibawi Rivera
From: Eric Pettersen <pett at cgl.ucsf.edu>
Sent: Tuesday, March 9, 2021 1:51 PM
To: Rade Jibawi Rivera <rj687 at mynsu.nova.edu>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] ORCA XYZ FILES

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<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FXYZ_file_format&data=04%7C01%7Crj687%40mynsu.nova.edu%7Cf065e9bd1b934322e67c08d8e32c541f%7C2c2b2d312e3e4df1b571fb37c042ff1b%7C1%7C0%7C637509127252002486%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=CIEiVvDHOeetBP%2F4HNRMYhSdtZ9s6Vg2W%2Fr5aHNo5aU%3D&reserved=0> 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<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.cgl.ucsf.edu%2Fchimera%2Fcurrent%2Fdocs%2FContributedSoftware%2Fmovie%2Fframemovie.html&data=04%7C01%7Crj687%40mynsu.nova.edu%7Cf065e9bd1b934322e67c08d8e32c541f%7C2c2b2d312e3e4df1b571fb37c042ff1b%7C1%7C0%7C637509127252002486%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=b63SIzxDGLoOkb1oGcso5MU5X7ZajV0A5Oc5eqp3cUs%3D&reserved=0>).
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 Pettersen
UCSF Computer Graphics Lab

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


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 at cgl.ucsf.edu<mailto:Chimera-users at cgl.ucsf.edu>
Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=04%7C01%7Crj687%40mynsu.nova.edu%7Cf065e9bd1b934322e67c08d8e32c541f%7C2c2b2d312e3e4df1b571fb37c042ff1b%7C1%7C0%7C637509127252012480%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=LNHOHNlNw1AXAuUURxfPsnPnDZVmlMIoBXU1QDBGGgw%3D&reserved=0>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210310/630d48d7/attachment-0001.html>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: trajectory_5nm cube XYZ.txt
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210310/630d48d7/attachment-0001.txt>

More information about the Chimera-users mailing list