Test insertion codes

[ijpulidos]

• Test insertion codes. For example ALA PDB with insertion codes.

Just take a PDB with insertion codes and check we can run it in our protein mutation protocol. We would just pick the first insertion code to be used.

[ijpulidos]

I may be misunderstanding what insertion codes are supposed to do, but I was expecting that I could do different rotamers and separate them using insertion codes. PyMOL and OpenMM (PDBFile) seem to disagree with what I did, though. Please check the attached file, the important part being:

ATOM      7  N   ASP A   2       0.787   0.621  -0.157  1.00  0.00           N
ATOM      8  H   ASP A   2       0.859   0.517  -1.158  1.00  0.00           H
ATOM      9  CA  ASP A   2       2.047   0.800   0.570  1.00  0.00           C
ATOM     10  HA  ASP A   2       1.844   1.218   1.554  1.00  0.00           H
ATOM     11  CB  ASP A   2       2.721  -0.570   0.745  1.00  0.00           C
ATOM     12  HB2 ASP A   2       2.848  -0.711   1.820  1.00  0.00           H
ATOM     13  HB3 ASP A   2       3.733  -0.505   0.342  1.00  0.00           H
ATOM     14  C   ASP A   2       2.979   1.781  -0.171  1.00  0.00           C
ATOM     15  O   ASP A   2       2.852   1.973  -1.378  1.00  0.00           O
ATOM     16  CG  ASP A   2       2.114  -1.877   0.199  1.00  0.00           C
ATOM     17  OD1 ASP A   2       1.032  -1.872  -0.434  1.00  0.00           O
ATOM     18  OD2 ASP A   2       2.778  -2.921   0.392  1.00  0.00           O
ATOM     19  N   ASP A   2A      0.785   0.642  -0.161  1.00  0.00           N
ATOM     20  H   ASP A   2A      0.301  -0.244  -0.139  1.00  0.00           H
ATOM     21  CA  ASP A   2A      2.048   0.801   0.556  1.00  0.00           C
ATOM     22  HA  ASP A   2A      1.829   1.235   1.550  1.00  0.00           H
ATOM     23  CB  ASP A   2A      2.741  -0.576   0.755  1.00  0.00           C
ATOM     24  HB2 ASP A   2A      3.228  -0.893  -0.185  1.00  0.00           H
ATOM     25  HB3 ASP A   2A      1.998  -1.358   0.983  1.00  0.00           H
ATOM     26  C   ASP A   2A      2.960   1.765  -0.163  1.00  0.00           C
ATOM     27  O   ASP A   2A      3.125   1.708  -1.388  1.00  0.00           O
ATOM     28  CG  ASP A   2A      3.795  -0.631   1.870  1.00  0.00           C
ATOM     29  OD1 ASP A   2A      4.800   0.105   1.793  1.00  0.00           O
ATOM     30  OD2 ASP A   2A      3.636  -1.446   2.803  1.00  0.00           O

But PyMol visualizes it as:

Which is clearly not what I intended. Also, OpenMM reads it similarly as:

In [1]: from openmm.app import PDBFile

In [2]: asp_insertion = PDBFile("ASP_capped_insertion.pdb")

In [3]: asp_insertion.topology
Out[3]: <Topology; 1 chains, 4 residues, 36 atoms, 36 bonds>

But in this case I cannot be sure that OpenMM knows how to handle insertion codes.

[ijpulidos]

I do think I'm misunderstanding what insertion codes are supposed to be, since it seems that in this example they just put them in sequence, instead of being on top of each other.

[IAlibay]

Insertion codes are completely separate residues (added sequentially).