[Chimera-users] ORCA XYZ FILES

[Eric Pettersen]

Hi Rade,
	I can tell you would want to visualize bonds breaking and forming with this trajectory (I was able to look at it in ChimeraX through a fairly involved procedure).  Assuming you go through the process that Elaine described for preparing the input for Chimera, the simplest way to get Chimera to check bonds each frame is to edit this file:

	<your Chimera installation>/share/Movie/gui.py

(on a Mac, <your Chimera installation> is Chimera.app/Contents/Resources).  Change line 75 of that file from:

	self.dynamicBonds = getattr(ensemble, 'dynamicBonds', False)

to:

	self.dynamicBonds = True

That will make every trajectory you read check bonds every frame.  It is possible to change it just for particular trajectories, but it's several more steps and even more arcane.

--Eric

> On Mar 10, 2021, at 2:36 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hello Rade Jibawi Rivera,
> As it says in the "startup and input" section of the link that Eric sent before, 
> <https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/movie/framemovie.html>
> 
> ...for XYZ you need each frame to be a separate file and you need to name the files so that they have numbers in the name, e.g. file00001.xyz, file00002.xyz, ... , file99999.xyz  (or however many frames that you have in your trajectory).  
> 
> Then you would start the MD Movie tool (Chimera menu: Tools... MD/Ensemble Analysis... MD Movie), specify input as XYZ format, and browse to enter the  names of the first and last input files in the input dialog, in the above example would be file00001.xyz and file99999.xyz
> 
> If ORCA cannot give you separate files you would probably need to write a script to do that.  I manually took the first three frames from your trajectory and saved them as files traj1.xyz, traj2.xyz, traj3.xyz attached to this message.  You can download them to your computer and then use them as an example input for a very short (3-frame) trajectory.  I tried this, they open fine in MD Movie as shown by the screenshots.
> 
> Then after your trajectory is being shown with MD Movie, you can change the window size, background color, etc. as you wish.  You can use the playback controller just to see how the trajectory looks.  Then when you are ready to record it as movie, choose from the MD Movie menu: File... Record a Movie as explained here:
> <https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#recording>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> <traj1.xyz><traj2.xyz><traj3.xyz>
> 
> Start MD Movie, change to XYZ format, browse to identify input files
> <Screen Shot 2021-03-10 at 2.30.48 PM.png>
> 
> Then the short trajectory of 3 frames is shown
> <Screen Shot 2021-03-10 at 2.32.05 PM.png><Screen Shot 2021-03-10 at 2.35.04 PM.png>
> 
> 
> 
> 
>> On Mar 10, 2021, at 1:46 PM, Rade Jibawi Rivera <rj687 at mynsu.nova.edu> wrote:
>> 
>> 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 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 at 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
>>> _______________________________________________
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>> 
>> <trajectory_5nm cube XYZ.txt>_______________________________________________
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