[phenixbb] Model_vs_data speed

Pavel Afonine pafonine at lbl.gov
Sun Oct 15 22:10:40 PDT 2017


I'm sorry it is slow, or slower than you expect. I'm sure technically it 
can run up to 10 seconds max per largest structure in PDB, as advertised in


if corresponding code is appropriately refactored (making most use of 
above paper); plus time taken by phenix.molprobity.

Unfortunately, I'm away till October 26, and then will be at the 
workshop till November 6th.

Others from the team (Dorothee, Oleg, Nigel, Billy, Vincent, Chris?) are 
encouraged to feel free to volunteer to address obvious runtime 
bottlenecks in this code.

All the best,

On 10/15/17 04:35, Eric Williams wrote:
> I'm having a devil of a time getting model_vs_data to run in a timely 
> fashion. Running the latest stable Linux build on Ubuntu 14.04 takes 
> on the order of 3 minutes per structure. That wouldn't be so bad if I 
> weren't trying to run it on every entry in the PDB. Is it just a 
> limitation of Python? SFCheck, which I think is written mostly in 
> FORTRAN, runs in a few seconds. Any help anyone could offer would be 
> appreciated. Thanks. :)
> Eric

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