[Chimera-users] make one chain from two chains ID in PDB

Eric Pettersen pett at cgl.ucsf.edu
Thu Mar 4 11:50:38 PST 2010

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 Pettersen
                         UCSF Computer Graphics Lab

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