[phenixbb] pdb help

Pavel Afonine pafonine at lbl.gov
Fri May 19 12:35:34 PDT 2017


I afraid for very large molecules it may take a lot of memory. This is 
because internally the procedure generates and accumulates hundreds if 
not thousands maps.. You can try to make these maps smaller by changing

which may diminish the efficacy of the protocol but that's the only 
suggestion I have (apart from trying it on a "bigger" computer).


On 5/18/17 14:28, jp d wrote:
> hi,
> phenix version 1.11.1-2575
> FEM has crashed a few times for me .
> i have tried using various parameters (resolution_factor=1./3, use_resolve=False) ,
> but it will max out my RAM (24G) and get into swap space.
> It gets very memory intensive, i think thats why it crashed.
> Do you have any suggestions to try ?
> i previously had a similar problem with a pdb using conflicting chain assignments,
> but this pdb doesn't use chains
> thanks
> jpd
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