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. http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts 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. Tom -------- Original Message -------- Subject: [Chimera-users] loading atomic coordinates without drawing or calculating bonds From: Veysel Berk To: chimera-users@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