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)?
I have also seen, since this since threading was introduced, and in some of these parts of the structure, you can straighten forever, the straighten tool will allow the structure to continue to rotate around these points indefinitely.
I have also seen this since threading was introduced, and in some of these parts of the structure, you can straighten forever, the straighten tool will allow the structure to continue to rotate around these points indefinitely.
oops, sorry for double (now triple) post, timed out, so i refreshed and corrected typo. I did not know why certain parts rotated forever, but after seeing this post, the parts that do are the same way.
The fix for this went out in the update today. Please reopen if you continue to notice this problem.
From your post in the other case (http://fold.it/portal/node/987708) it looks like this is not resolved.
I've posted another update that should take car of it this time.
