density scoring

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    • August 29, 2020 at 11:54 am #3558
      Anonymous

        Hi,

        I have some questions about setting for scoring and weights. That would be really helpful if someone could answer the questions.

        1.

        I looked into the folder>   Rosetta/main/database/scoring,  there are loads of score files.I’m wondering  How to choose the right one.

        Should I just use one for all applications? For example, If I use Rosetta3.12, should I use  ref2015.wts for relax, loopmodel,etc?

        Could someone please kindly explain to me what’s the difference between these score files?

        for example 

        ref2015_cart_cst.wts,

        ref2015_cart.wts,

        ref2015_cst.wts,

        ref2015_soft.wts

        ref2015.wts

        remodel_cen.wts

         

        2.

        I’d like to use rosetta to model a loop region based on EM density.

        I got a flag file from my colleague, in which -edensity:whole_structure_allatom_wt is 0.05. -score:weights score13_env_hb. (He used Rosetta 3.7)

        But I found one online tutorial updated on 2018 , the setting is -edensity_dens_fast_wt 35.  Does the difference  come from different rosetta version?

         

         

        Thanks a lot,

        Tian

         

      • August 31, 2020 at 5:23 am #15469
        Anonymous

          Hello,

          To tell the difference between the different score files, I suggest opening them and comparing them!

          ie the difference between ref2015_cart_cst and ref2015_cart is: 


          
1c1
          
< # beta_nov15
          
---
          
> # ref2015_cart_cst
          
29a30,34
          
> coordinate_constraint 1.0
          
> atom_pair_constraint 1.0
          
> angle_constraint 1.0
          
> dihedral_constraint 1.0
          
> res_type_constraint 1.0

           

          so the ref2015_cart_cst just sets the constraint weights to 1. sort of a shortcut way.

           

          I’m not sure of the which  tutorials you are referencing but I would suggest you follow the tutorials at https://dimaiolab.ipd.uw.edu/software/ for loop building!

           

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