Re: [phenixbb] Output for den optimization runs

My only other suggestion would be to try and use Cartesian simulated annealing instead. Sometimes I've found that this method performs better. Jeff On Mon, Jan 9, 2012 at 3:44 PM, Francis E Reyes wrote:

Any other recommendations for the simulated annealing run besides lowering the starting temperature when you have a model that's mostly (90%) placed?

Thanks!

F

On Jan 9, 2012, at 3:37 PM, Jeff Headd wrote:

...

Hi Francis,

At the moment the only way to change the starting temperature is to do so in the 'tardy' scope. This would look like:

refinement {  tardy {    start_temperature_kelvin = 2500    final_temperature_kelvin = 300  }

Adding DEN-specific control is on my to-do-list.

Jeff

On Mon, Jan 9, 2012 at 2:23 PM, Francis E Reyes wrote:

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Is there an option to specify the starting torsion simulated annealing temperature when den.optimize=True ?

F

On Jan 9, 2012, at 10:45 AM, Jeff Headd wrote:

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Hi Francis,

Each DEN optimization step outputs a lot of information, so at present the code suppresses that information and only a summary will be printed at the conclusion of optimization.

I can add an option for verbose output, though if the job is running on multiple cores the logs would need to be written after all jobs have completed for the output to be readable.

Jeff

On Mon, Jan 9, 2012 at 9:39 AM, Francis E Reyes wrote:

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Is there a refine.log for each den (gamma, weight) optimization? I can't seem to find one anywhere and I'm curious to see how it's doing.

Thanks!

F

--------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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