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how to use density tools with current energy function

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how to use density tools with current energy function
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Hi,

I'm following the tutorial on electron density tools: https://docs.rosettacommons.org/demos/latest/public/electron_density_structure_refinement/structure_refinement

I started with scenario 0. Example 0A works, but the scores I get are different from the ones in the output example. Then example 0B fails with an error: "To use the 'talaris2013_cart' score function please use the -restore_talaris_behavior flag on the command line." I've tried doing this, but the error persists.

I'm guessing that the tutorial is old and the score function definition in the xml file ( <ScoreFunction name="dens" weights="talaris2013_cart">) is not compatible with the current scoring function. Is this correct? Is there an updated version of the tutorial, or what should I use to make it work? I am using Rosetta 3.13


 

 

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Wed, 2024-07-10 09:37
xfradera

talaris2013 is indeed old. The current default scorefunction is ref2015, and there's some "experimental" scorefunctions which are availible which aim to improve it.

For updated demos using density, I'd recommend looking at Frank DiMaio's page at https://dimaiolab.ipd.uw.edu/software/

P.S. We're updating the site, and as part of that we're moving the forums to Github Discussions. It's likely best to direct any follow-up questions there.

Wed, 2024-07-10 15:13
rmoretti