Known Bugs

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[edit] 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.

[edit] 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.

[edit] energy calc

A single energy calc command causes two TOTALE lines to be printed, further these do not always agree.


[edit] 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).

[edit] 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

[edit] Various

"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

[edit] Residues listed out of order cause issues for chain assignment

Example 2CJM - modified residue listed at end, causes issues for assignment (also missing template)

[edit] Not a bug but improvements that could be made

Represent symmetry transformations as augmented transformation matrices, as it would simplify the math incredibly, see:
http://en.wikipedia.org/wiki/Transformation_matrix#Affine_transformations
http://en.wikipedia.org/wiki/Homogeneous_coordinates#Use_in_computer_graphics

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