Rosetta Resfile header

[Anonymous]

I have been using Rosetta design for quite a while but I did not pay attention to what Resfile header would do. I looked for descriptions and examples files different people have shared and used and I am unable to understand when I should specify NATRO or NATAA in the header?

I want to perform different tasks. For example:

1) Mutate specific residue to ALLAA and I use header like:

NATRO

start

30 H ALLAA

whereas, I found someone using following header:

NATAA

USE_INPUT_SC

start

79 C ALLAA

and if I want to mutate single residue or multiple residues to one particular residue, I use:

NATAA

start

53 C PIKAA A

56 C PIKAA A

but I dont know which header I should use. From header definations I collected following information:

The default NATAA will allow non-mutated residues to repack around your mutations, whereas the default ALLAA would have caused all residues everywhere to be designed, resulting in many mutations (not just the 2 you want).

NATRO # default command that applies to everything without a non- default setting; do not repack

What I understand NATAA repack all residues around mutated residue but what NATRO does is unclear to me?

 

I will be looking forward for your kind response

Mustafa

[Anonymous]

So the header line(s) above the “start” is the “default” – it applies to all residues which are not otherwise specified under the “start”. The designations/commands for the header line are identical to the designations for each individual amino acid.

Regarding NATRO/NATAA/PIKAA/ALLAA, each of them specifies a different amount of flexibility:

ALLAA means that all amino acids should be considered at that position. That is, the packer will take the rotamers for all 20 canonical amino acids, throw them into a big pot and (hopefully) pick out the one which is the lowest energy.

PIKAA does something similar, but allows you to specify a particular subset of amino acids to take rotamers from.

NATAA means to only take the rotamers from the starting (“native”) amino acid. The sidechain for those positions are allowed to vary and repack, but they’re not allowed to change to a residue identity different from the starting amino acid.

NATRO takes it a step farther. It tells the packer that it should only consider the starting (“native”) rotamer at that position. Don’t change the identity, and don’t even change the conformation. Only take that one starting rotamer.

 

So what command you want in the header depends on what behavior you want for residues not explicitly specified under the “start” line. If you want then to stay absolutely fixed, and not repack or move in any fashion, use NATRO. If you just want them to stick to their current identity, but would like them to be able to change conformation, use NATAA.

Alternatively, if you are doing a general redesign, but have certain residues you don’t want to change, you can set up your resfile with the header being ALLAA (meaning that most of the residues will be designed), and then place the specific residues you want to hold fixed as NATRO or NATAA in the lines after “start”.

[Anonymous]

Thanks a lot for such comprehensive response.

I want to know if there are steric clasches in the native structure, would it be advisable to use NATAA instead of NATRO in the header.

When I use NATAA as header and ALLAA after start,

NATRO

start

30 H ALLAA

I get alanine residue picked up from the pool which gives least energy:

 108     SER        ALA   

 108     SER        ALA   

 108     SER        ALA   

 108     SER        ALA   

 108     SER        ALA   

rostta.out

0          20000  all_scan       35          fa_ref2015          ddG   -12.372470

1          40000  all_scan       35          fa_ref2015          ddG   -15.133570

2          60000  all_scan       35          fa_ref2015          ddG   -11.990080

3          80000  all_scan       35          fa_ref2015          ddG   -13.458700

4         100000 all_scan       35          fa_ref2015          ddG   -10.458390

 

and if I use

NATAA

start

108 H PIKAA A

I get different energy score:

0          20000  Ala_scan       35          fa_ref2015          ddG    -2.908880

1          40000  Ala_scan       35          fa_ref2015          ddG    -2.893370

2          60000  Ala_scan       35          fa_ref2015          ddG    -3.322820

3          80000  Ala_scan       35          fa_ref2015          ddG    -3.566730

4         100000  Ala_scan       35          fa_ref2015          ddG    -3.139640

 

Does this mean choice of header is giving me this difference in energies?

kind regards

Mustafa

 

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