[Chimera-users] Models or chain

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 29 15:30:13 PDT 2008

Hi Hernando,
Sorry, Chimera does not have an option for changing chain IDs.

However, in Chimera I find it more convenient to work with structures  
read as multiple models as opposed to multiple chains in a single model:

- you can easily toggle which are shown and which are active (movable  
with the mouse) using the Model Panel

- you can move one relative to another, whereas you cannot move one  
chain relative to another chain in the same model

- just like different chains, you can specify them independently in  
commands, rainbow-color to give each its own color, etc.  In commands,  
the different models read from a single PDB file are specified as  
#0.1, #0.2, ... (and residues within them specified using something  
like #0.1:23,350-355 )

- further, each model can include several of its own chains, and it is  
OK if another model in the same file also uses the same chain IDs, as  
they are still distinguishable (#0.1:23.a is different than #0.2:23.a)

Now I'm actually disappointed when a Web server gives me multiple  
models as different chains in a single model, because it is less  

I do agree there may be situations in which you want the models as  
different chains, such as for input to another program, but currently  
Chimera does not include that type of editing.
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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