On Jun 11, 2022, at 11:21 PM, Shubham Devesh Ramgoolam via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

I just wanted to specify that I am using the nogui mode of chimeraX for the computation.

Shubham.

---

From: Shubham Devesh Ramgoolam
Sent: June 12, 2022 1:38 AM
To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: Trajectory computation slowing down overtime

 

Hi all,

I hope you are doing well.

 

I have a Python script for analyzing specific residue pairs for every frame in a trajectory.

It does so, by using 2 for loops:

For frame in list_frames:

               Set current frame to frame

               For pair in specific_residue_pairs:

                              Do computation

 

The computation involves defining geometric objects(centroids, axes, planes) and performing calculations with them(distance, angles).

The issue here is that as we move further in list_frames, the computation takes longer and longer. There is a somewhat linear increase in computation time, as illustrated below:

 

<E0E35EA38D4345BE98A480EB08BE8CEC.png>

 

Is there a way to maintain the same computation time for every frame in the trajectory?

 

Regards,

Shubham Ramgoolam

Sent from Mail for Windows

 

_______________________________________________
ChimeraX-users mailing list
ChimeraX-users@cgl.ucsf.edu
Manage subscription:
https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users