[chimerax-users] Issue with loading large trajectory topology and coordinate file

[Eric Pettersen]

Hi Shubham,
	 I think the issue is more the 62 MB PSF file than the DCD file.  Though both are read by Python, the PSF file is much more complicated, slower to parse, and requires setting up a complex atomic system.  On my personal machine, reading a PSF file takes about 1.75 seconds per MB, so your PSF file would take ~109 seconds to read on my machine.  Reading the DCD file is much faster, particularly if start/end/step is being used.
	If you have your system in PDB or mmCIF format, using that instead of the PSF will be much faster.  For instance, opening 30000 atom PSF file takes  7.8 seconds on my machine, but opening the equivalent PDB file only takes .7 seconds.  If you don't have the equivalent file, you could open one frame of your trajectory and save that as PDB.  At least opening it in later sessions will be faster.  In case you don't know, if you have the PDB structure open as model #1 you would read in the trajectory frames with:

	open blah.dcd structure #1

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

	

> On Jul 12, 2022, at 10:28 AM, Shubham Devesh Ramgoolam via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi all,
> I hope you are doing well.
>  
> I have a PSF file of size 62 MB and a DCD coordinate file of size 423 MB that I am trying to load in chimeraX. However, chimeraX remains unresponsive during the loading process.
>  
> As such, I tried loading a subset of the coordinate file using start stop step option. However, this did not fix the issue. This is an example of the command I used: open myfile.psf coords file.dcd start 1 stop 10 step 2
>  
> Is there an alternative approach I could use?
>  
> (I don’t know if this is relevant or not but whenever I closed and re-opened chimeraX after it became unresponsive, it did not ask me to send a bug report.)
>  
> UCSF ChimeraX version: 1.5.dev202206290845 (2022-06-29)
> OS: Windows 10
>  
> Regards,
> Shubham Ramgoolam
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows
>  
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20220712/ae2f7487/attachment.html>