Weird backbone atom placement
|Opened on:||Wednesday, March 17, 2010 - 22:36|
|Last modified:||Thursday, May 13, 2010 - 18:33|
See attachment: why is the carbonyl oxygen clashing into the -NH part of the backbone, and why isn't the clashing score in the negative thousands when this is happening? Even worse is the fact that rebuilding (with one band placed on the oxygen into one direction and another band placed on the nitrogen into the opposite direction) is insufficient to solve the problem, and neither does straightening the helix (in fact, the misplaced oxygen would prevent the straightening process from being done correctly).
This is not the first time that this has happened to me. Coincidentally, this bug has never been observed until threading became available, however. I wonder if it's caused by the direct copying of the backbone (i.e. forcing very non-ideal torsion angles)?