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