[Chimera-users] loading atomic coordinates without drawing or calculating bonds
goddard at cgl.ucsf.edu
Wed Aug 5 10:34:51 PDT 2009
You will have a rough time trying to open 1 million atoms in Chimera
because it is very memory inefficient, taking about 2 Kbytes per atom.
So 1 million atoms will take about 2 Gbytes and this is unlikely to work
with 32-bit versions of the program. Only the 64-bit linux version is
likely to handle it.
You are probably better off making a volume data set from your million
points. There is a Python Chimera script called xyzmap.py you can use
to do this.
Each point is treated as a Gaussian of specified width. After making
the map you can save it with the volume dialog File / Save Map As...
menu entry or the volume command.
-------- Original Message --------
Subject: [Chimera-users] loading atomic coordinates without drawing or
From: Veysel Berk
To: chimera-users at cgl.ucsf.edu
Date: 8/5/09 2:52 AM
> I am trying to load a large atomic coordinates file in xyz format.
> The atomic coordinates are meaningless to crystallography in terms
> of distances of atoms and as a result, while chimera try to load
> the coordinate and calculate the bonding between atoms, it crashes
> or suspends for ever. The data is from single molecule
> localization experiments where I want to use chimera to visualize
> this 3D data by treating each localization as an atom. I am trying
> to load about a million atoms.
> Is it possible to turn off automatic bonding calculations and only
> show atoms without bonds to prevent crashing? or does anyone know
> any simple method or software to convert atomic coordinates into
> voxel map which I can use in volume visualizer module of chimera
> without worrying about bond calculations?
> Thanks in advance,
> Veysel Berk
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