Hi Christos, I optimized the memory use of split map about 3 weeks ago. You can try this improved version by downloading the current Chimera daily build: http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Still it will need to allocate a full map for each color and that can use a great deal of memory. If your map is 1 Gbyte and you have several colors it will not work with a 32-bit version of Chimera. Although you have 4 Gbytes of memory, some is used by the shared libraries, operating system, stack, Chimera code, and data. You will be lucky to get 2 Gbytes of data in memory before you run out of address space (32-bit = 4 Gbytes). There simply will be no large enough chunk of the 32-bit address space to put a copy of the map in. To use more than about 2 Gbyte of data in memory you have to use a 64-bit version of Chimera. One is available for Linux. Tom Tom Goddard wrote:
Hi Thomas,
The error you got using the Chimera split map command "MemoryError" means your machine didn't have enough memory. The split map code is quite inefficient, allocating 3 * (number of grid points) floats and that allocation failed for you. I've optimized that code a little so for maps larger than 16 Mvoxels it works plane by plane avoiding that big allocation. You still may run out of memory because each color becomes a new full-size map in memory. If you have many colors that can be a lot of memory.
The optimized code will be in tonight's Chimera builds (if they succeed):
http://www.cgl.ucsf.edu/chimera/alpha-downloads.html
Tom