[Chimera-users] opening large xyz file

Eric Pettersen pett at cgl.ucsf.edu
Mon Jun 27 10:59:06 PDT 2016

Hi Michał,
	Yeah, Chimera is trying to find the connectivity between your 66,000 atoms in an N squared manner, which will take close to forever.  There is no way to prevent the connectivity search without editing Chimera’s code.  If you are willing to edit the code, change line 80 of <your Chimera>/share/ReadXYZ/__init__.py from:




(i.e. comment out the call to compute the connectivity).  Make sure to keep the indentation the same.  If you are feeling fancy, you might instead change that line to:

	if len(m.atoms) < 10000: connectMolecule(m)

which will allow to the connectivity to be computed for smaller structures (< 10000 atoms) but skip it for structures as large as yours.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Jun 27, 2016, at 7:30 AM, Michał Kadlof <m.kadlof at cent.uw.edu.pl> wrote:
> Hello,
> I'm trying to open a xyz file that contain ~66000 entries (1.7 MB). Chimera hangs and rapidly allocates huge amounts of RAM (more than 60 GB) which is close to limits of my PC, is it normal?
> Is there any "rescue mode opening" that wouldn't search for bonds to render and/or would show particles as dots or 2D disks instead of ball?
> My system is spatially small and probably Chimera is trying to search all-to-all particles to render bonds between them, but I do not need this. Is there any way to prevent this behaviour?
> --
> best
> Michał
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