 |
 |
Hello, I'm working on a structure using coot, and I have a peculiar problem. Searching www didn't quite provide me with an answer, hence requesting more knowledgeable users for some help. Background: The structure has 2 chains, Chain A and Chain B. Chain B has all the residues that should be present according to our sequence, and the numbering on both chains are complete. Problem: 1) Chain A has a couple of residues missing. The numbering shows 231 232 234. Clearly marking out the spot where the residue is missing. Sequence shows that there is an aspartic acid missing in position 233. Problem is - both 232 and 234 are connected quite normally, inserting a terminal residue at 232 (alanine at first) results in absolutely weird connections. Deleting specific atoms in the backbone on the protein at that position (between 232 and 234) don't quite help either - as that results in 234 missing a peptide bond. 2) At some points, there is no backbone -by which I mean - lets say residue 100 and 101 side chains are showing up (and have appropriate electron density). What is missing is the peptide bond that connects these two residues (again - electron density for the backbone is present). Is there a way to fix this? Can someone walk me through the solution to this problems? Thank You, Alok Shenoy