Energy scores of D-amino acids

[Anonymous]

I used PyMOL and Maestro to invert the chirality of single L-amino acids into D-amino acids, as well as all L-residue polypeptide to all D-residue polypeptides. Even though they are mutually mirror images, but D-amino acids and D-polypeptides all have remarkably higher energy scores than their counterparts by using PyRosetta scoring protocol. May I ask what are some possible reasons for this difference? I am wondering whether it is caused by computational error or more delicate design, such as strong and weak nuclear forces, in Rosetta tool.

[Anonymous]

What version of Rosetta are you using? There were some bugs with in D-amino acid scoring which should (*knock wood*) be fixed with the most recent weekly release.

[Anonymous]

What version of Rosetta are you using? There were some bugs with in D-amino acid scoring which should (*knock wood*) be fixed with the most recent weekly release.

[Anonymous]

What version of Rosetta are you using? There were some bugs with in D-amino acid scoring which should (*knock wood*) be fixed with the most recent weekly release.

[Anonymous]

Did your protocol also invert the backbone and sidechain torsions of these residues? A D-amino acid with phi, psi of (-60, -40) is quite strained.

 

Are the high energies mostly in rama and fa_dun?

[Anonymous]

Did your protocol also invert the backbone and sidechain torsions of these residues? A D-amino acid with phi, psi of (-60, -40) is quite strained.

 

Are the high energies mostly in rama and fa_dun?

[Anonymous]

Did your protocol also invert the backbone and sidechain torsions of these residues? A D-amino acid with phi, psi of (-60, -40) is quite strained.

 

Are the high energies mostly in rama and fa_dun?

[Anonymous]

To flip the chirality of a peptide properly in Rosetta, you need to do BOTH of the following:

1. Mirror all xyz coordinates (which also effectively inverts all torsion values).

2. Convert the L residue types into D residue types.  (If you just mirror coordinates, Rosetta thinks that you still have L-amino acids with weird geometry).

You can do this manually, but it’s easier to use the FlipChirality mover, which does both steps for you (https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/FlipChiralityMover).

I can say with great certainty that Rosetta’s scoring, with the talaris2013, talaris2014, or beta_nov15 scorefunctions, is fully symmetric: mirror-image structures yield identical scores, if you mirror the structures properly.

[Anonymous]

To flip the chirality of a peptide properly in Rosetta, you need to do BOTH of the following:

1. Mirror all xyz coordinates (which also effectively inverts all torsion values).

2. Convert the L residue types into D residue types.  (If you just mirror coordinates, Rosetta thinks that you still have L-amino acids with weird geometry).

You can do this manually, but it’s easier to use the FlipChirality mover, which does both steps for you (https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/FlipChiralityMover).

I can say with great certainty that Rosetta’s scoring, with the talaris2013, talaris2014, or beta_nov15 scorefunctions, is fully symmetric: mirror-image structures yield identical scores, if you mirror the structures properly.

[Anonymous]

To flip the chirality of a peptide properly in Rosetta, you need to do BOTH of the following:

1. Mirror all xyz coordinates (which also effectively inverts all torsion values).

2. Convert the L residue types into D residue types.  (If you just mirror coordinates, Rosetta thinks that you still have L-amino acids with weird geometry).

You can do this manually, but it’s easier to use the FlipChirality mover, which does both steps for you (https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/FlipChiralityMover).

I can say with great certainty that Rosetta’s scoring, with the talaris2013, talaris2014, or beta_nov15 scorefunctions, is fully symmetric: mirror-image structures yield identical scores, if you mirror the structures properly.

[Anonymous]

The version I used is Pyrosetta 3 on Windows OS

[Anonymous]

The version I used is Pyrosetta 3 on Windows OS

[Anonymous]

The version I used is Pyrosetta 3 on Windows OS

[Anonymous]

Yes, the protocol inverts both backbone and sidechain to make a mirror image all D-peptide. The high energies are rama, fa_dun, and p_aa_pp

[Anonymous]

Yes, the protocol inverts both backbone and sidechain to make a mirror image all D-peptide. The high energies are rama, fa_dun, and p_aa_pp

[Anonymous]

Yes, the protocol inverts both backbone and sidechain to make a mirror image all D-peptide. The high energies are rama, fa_dun, and p_aa_pp

[Anonymous]

Rosetta and PyRosetta is in active development, and bugs are fixed on a regular basis. “PyRosetta3” is a bit too vauge (and the most recent versions are PyRosetta4). What do you get when you do something like:

print pyrosetta.version()

(Or `print(pyrosetta.version())` if you’re using Python3) 

You should get something like 

PyRosetta-4 2017 [Rosetta 2017 59441:64c90c89271ea96b863085358daee1510ee9499f  2017-05-04 20:51:53 -0400]

If the date at the end is earlier than mid 2016 or so, I’d highly recommend you update to the most recent version, so you get all the D-aa bug fixes. Depending on what you’re doing, you may even need to update if the date is before Oct 2016.

 

Alternatively, there should be a string of digits which are printed out when you call the init() function, and those would work as a version designation as well,  though one that’s a little harder to descipher.

 

 

[Anonymous]

Rosetta and PyRosetta is in active development, and bugs are fixed on a regular basis. “PyRosetta3” is a bit too vauge (and the most recent versions are PyRosetta4). What do you get when you do something like:

print pyrosetta.version()

(Or `print(pyrosetta.version())` if you’re using Python3) 

You should get something like 

PyRosetta-4 2017 [Rosetta 2017 59441:64c90c89271ea96b863085358daee1510ee9499f  2017-05-04 20:51:53 -0400]

If the date at the end is earlier than mid 2016 or so, I’d highly recommend you update to the most recent version, so you get all the D-aa bug fixes. Depending on what you’re doing, you may even need to update if the date is before Oct 2016.

 

Alternatively, there should be a string of digits which are printed out when you call the init() function, and those would work as a version designation as well,  though one that’s a little harder to descipher.

 

 

[Anonymous]

Rosetta and PyRosetta is in active development, and bugs are fixed on a regular basis. “PyRosetta3” is a bit too vauge (and the most recent versions are PyRosetta4). What do you get when you do something like:

print pyrosetta.version()

(Or `print(pyrosetta.version())` if you’re using Python3) 

You should get something like 

PyRosetta-4 2017 [Rosetta 2017 59441:64c90c89271ea96b863085358daee1510ee9499f  2017-05-04 20:51:53 -0400]

If the date at the end is earlier than mid 2016 or so, I’d highly recommend you update to the most recent version, so you get all the D-aa bug fixes. Depending on what you’re doing, you may even need to update if the date is before Oct 2016.

 

Alternatively, there should be a string of digits which are printed out when you call the init() function, and those would work as a version designation as well,  though one that’s a little harder to descipher.

 

 

[Anonymous]

Thank you. It is very helpful. I always used the most revent version of pyrosetta3, but it is still 2014. I will used pyrosetta4 from now on.

[Anonymous]

Thank you. It is very helpful. I always used the most revent version of pyrosetta3, but it is still 2014. I will used pyrosetta4 from now on.

[Anonymous]

Thank you. It is very helpful. I always used the most revent version of pyrosetta3, but it is still 2014. I will used pyrosetta4 from now on.

[Author]

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