[phenixbb] Memory and CPU usage

Nathaniel Echols nechols at lbl.gov
Sat Jul 21 09:55:02 PDT 2012

On Sat, Jul 21, 2012 at 9:43 AM, Pavel Afonine <pafonine at lbl.gov> wrote:
> I see (d_min/3) in your formula above as a grid step factor. Most of map
> calculations in phenix.refine and tools around it use (d_min/4). Putting
> this into your formula
> map_size = 8 * a * b * c * (d_min/4)^3
> will obviously result in a smaller map, which isn't true. Am I missing
> something?

No, I am - the final multiply operation should be a divide:

map_size = 8 * a * b * c / (d_min/resolution_factor)^3

But the resolution_factor is inconsistent - for the FFT structure
factors calculation (which is unavoidable), we are definitely using
1/3 (I assume for speed reasons).  For most of the other optional
tasks like rotamer correction and filling missing F-obs, it's 1/4.


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