From Jacobson Lab Wiki
 Excluded Atoms from Sequence
The "load seq" command does not correctly assign excluded atoms, namely numex(i+1) is not necessarily greater than numex(i) for all i.
 More informative error message
For the "Parameters not found for residue/molecule" outputting the residue type (ie. pro/het/ion) would be very nice. This would help differentiate between incorrect assignment of residue type and missing templates.
 energy calc
A single energy calc command causes two TOTALE lines to be printed, further these do not always agree.
 Missing Symmetry Operators
Missing symmetry operators can now be created with the pdb2sym script that lives in the scripts directory. Just drop the output file in data/space_groups. We will need to figure out a way of representing space groups that have funny characters in the names (i.e. slashes).
 Missing Protein Residue Templates
KWS(|b|e) - 3UNV
M3L(|b|e) - 3ME9
D-amino acids - 3FHV - theoretically could use phi-psi information from the corresponding L-amino acids, reflected
ALY - acetylated lysine 2YBG
"Cannot find _C5A in DCB" - 3RJJ, 3MBY
"Cannot find _CAO in DGB" - 3JPS
residue FGA - 3D2Y, namely fails to build chain B
resname TPQ - 1RJO
 Residues listed out of order cause issues for chain assignment
Example 2CJM - modified residue listed at end, causes issues for assignment (also missing template)
 Not a bug but improvements that could be made
Represent symmetry transformations as augmented transformation matrices, as it would simplify the math incredibly, see: