**10**wrote:

So I am trying to fold a primary structure using only the torsion angles from a natural protein's crystal structure. But I found this strange phenomena, which I cannot understand nor explain. My protocol is as follow:

I am taking a normal protein (figure 1)

Then I take the phi and psi torsion angles of each residue

Then I assemble a totally new flat amino acid chain, a primary structure, with the same original amino acid sequence (figure 2)

Then I change each residue's torsion angles to the torsion angles of the original protein from figure 1. I do this sequentially: residue 1, then residue 2, then residue 3 etc...

Theoretically I should be getting the same original structure back right? but I instead get a messed up structure (figure 3) even though all the torsion angles are

**EXACTLY**the same (check the file Angles.txt that shows separate measurements of each structure giving back**exactly**the same torsion angles).

So the question is **why** do I get this messed up structure, even though I use EXACTLY the same torsion angles (up to 9 decimal places - though I am only showing 3 decimal places for clarity).

Anyone can help me understand the issue? Is there something else I should include in my build other than torsion angles?

```
PHI Angles PSI Angles
BEFORE AFTER BEFORE AFTER
res 1 : 0.0 = 0.0 158.944 = 158.944
res 2 : -133.036 = -133.036 131.63 = 131.63
res 3 : -116.506 = -116.506 121.937 = 121.937
res 4 : -104.034 = -104.034 117.857 = 117.857
res 5 : -91.88 = -91.88 110.368 = 110.368
res 6 : -117.482 = -117.482 26.777 = 26.777
res 7 : -68.934 = -68.934 137.678 = 137.678
res 8 : 87.321 = 87.321 -12.42 = -12.42
res 9 : -90.092 = -90.092 139.446 = 139.446
res 10 : -96.65 = -96.65 147.198 = 147.198
res 11 : -54.743 = -54.743 149.75 = 149.75
res 12 : -90.664 = -90.664 25.177 = 25.177
res 13 : -55.218 = -55.218 -51.992 = -51.992
res 14 : -56.195 = -56.195 -43.852 = -43.852
res 15 : -64.895 = -64.895 -38.532 = -38.532
res 16 : -67.613 = -67.613 -45.091 = -45.091
res 17 : -61.604 = -61.604 -41.244 = -41.244
res 18 : -65.734 = -65.734 -43.604 = -43.604
res 19 : -65.9 = -65.9 -39.484 = -39.484
res 20 : -61.631 = -61.631 -44.855 = -44.855
res 21 : -63.75 = -63.75 -37.836 = -37.836
res 22 : -70.554 = -70.554 -43.277 = -43.277
res 23 : -64.617 = -64.617 -19.429 = -19.429
res 24 : -87.124 = -87.124 -13.039 = -13.039
res 25 : -72.555 = -72.555 -6.894 = -6.894
res 26 : 58.615 = 58.615 -169.69 = -169.69
res 27 : -63.408 = -63.408 -21.517 = -21.517
res 28 : -72.631 = -72.631 -17.643 = -17.643
res 29 : 66.031 = 66.031 -175.003 = -175.003
res 30 : 158.845 = 158.845 -159.158 = -159.158
res 31 : -129.889 = -129.889 132.223 = 132.223
res 32 : -123.581 = -123.581 118.737 = 118.737
res 33 : -106.945 = -106.945 144.557 = 144.557
res 34 : -129.689 = -129.689 129.539 = 129.539
res 35 : -93.157 = -93.157 119.117 = 119.117
res 36 : -127.144 = -127.144 158.788 = 158.788
res 37 : -111.018 = -111.018 24.26 = 24.26
res 38 : -161.233 = -161.233 149.981 = 149.981
res 39 : -63.585 = -63.585 -31.181 = -31.181
res 40 : -61.861 = -61.861 -43.522 = -43.522
res 41 : -64.088 = -64.088 -41.82 = -41.82
res 42 : -58.27 = -58.27 -46.947 = -46.947
res 43 : -59.426 = -59.426 -44.655 = -44.655
res 44 : -62.459 = -62.459 -42.601 = -42.601
res 45 : -61.049 = -61.049 -41.605 = -41.605
res 46 : -70.042 = -70.042 -37.405 = -37.405
res 47 : -64.006 = -64.006 -38.693 = -38.693
res 48 : -67.632 = -67.632 -40.142 = -40.142
res 49 : -65.242 = -65.242 -46.877 = -46.877
res 50 : -61.888 = -61.888 -49.239 = -49.239
res 51 : -43.502 = -43.502 -50.091 = -50.091
res 52 : -76.99 = -76.99 -5.108 = -5.108
res 53 : 79.836 = 79.836 34.694 = 34.694
res 54 : -113.987 = -113.987 150.501 = 150.501
res 55 : -83.139 = -83.139 150.361 = 150.361
res 56 : -153.067 = -153.067 160.032 = 160.032
res 57 : -147.001 = -147.001 168.855 = 168.855
res 58 : -147.48 = -147.48 151.234 = 151.234
res 59 : -139.45 = -139.45 131.529 = 131.529
res 60 : -90.944 = -90.944 106.94 = 106.94
res 61 : -90.123 = -90.123 -167.692 = -167.692
res 62 : -76.915 = -76.915 144.776 = 144.776
res 63 : 70.893 = 70.893 32.437 = 32.437
res 64 : 73.321 = 73.321 3.164 = 3.164
res 65 : -73.523 = -73.523 126.932 = 126.932
res 66 : -104.475 = -104.475 125.434 = 125.434
res 67 : -106.295 = -106.295 121.894 = 121.894
res 68 : -110.618 = -110.618 122.924 = 122.924
res 69 : -108.151 = -108.151 125.893 = 125.893
res 70 : -118.674 = -118.674 130.343 = 130.343
res 71 : -113.385 = -113.385 132.074 = 132.074
res 72 : -109.435 = -109.435 -34.442 = -34.442
res 73 : 178.142 = 178.142 -3.115 = -3.115
res 74 : -50.684 = -50.684 0.0 = 0.0
```

**20**• written 6 months ago by ac.research •

**10**

How are you doing about omega? https://en.wikipedia.org/wiki/Dihedral_angle#Proteins

180hmmm, good idea.

I added the function to include also the Omega angles which helped "a bit" check out the structure: new protein. But it is still corrupted, compare it with the original structure. what other variables would I need to include?

10:thinking_face_emoticon: I have no idea then.

Try superposition (select N-terminal 5 or 10 residues & A->align in PyMol) and check where discrepancy starts (ribbon mode or line mode will work).

180