On Mar 4, 2010, at 10:43 AM, Forbes J. Burkowski wrote:
Hi:
On Tue, 2 Mar 2010, Elaine Meng wrote:
I forgot to mention that when you change chain ID, you usually also need to change the residue numbering so that residues will be uniquely specifiable. For example, if you have two residues both numbered 10 in chain B, it may be difficult to do something to only one or the other in Chimera. Those editing servers allow renumbering in addition to changing the chain ID. Elaine
Just a note: If two chains are given the same chain ID, it is not clear how everything will properly work out, even with renumbering. I would imagine that Chimera would see the last residue in the first original chain as the part of a backbone that joins it to the first residue in the second original chain. Would this unfortunate connection occur?
Hi Forbes, Assuming that the TER card between the chains is retained, then no, Chimera will treat the two chains as completely separate entities despite the identical chain ID. This can be awkward in some interfaces that list chains since there will be two apparently- identical entries. If the TER card is removed then Chimera will treat them as one chain and will add a "missing structure" pseudobond connecting the last residue of one chain to the first residue of the other chain. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu