[Chimera-users] loading atomic coordinates without drawing or calculating bonds

Tom Goddard goddard at cgl.ucsf.edu
Wed Aug 5 10:34:51 PDT 2009

Hi Veysel,

  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   
 calculating bonds
From: Veysel Berk
To: chimera-users at cgl.ucsf.edu
Date: 8/5/09 2:52 AM
>     Hello,
>     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,
>     Bests,
>     Veysel Berk

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