density scoring

[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

 

[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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