[Chimera-users] Renaming chains in "combine" command

[Elaine Meng]

Hi Peter,
In my tests of "addaa", the new residue gets the same chain ID as the  
preceding residue.

For example, open 1zik, choose menu "Presets... Interactive 2 (all  
atoms)" then use commands:
rlabel :30
focus :30
addaa tyr,31,alpha :30.b
rlabel :31

the new residue is 31 in chain B attached to 30 in chain B.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html>

The "combine" command either copies a model or combines multiple  
models into one.  It does not change chain IDs within a single model.   
The only time it changes chain IDs is to avoid indistinguishable  
residues when combining multiple models into one model.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>

I don't know how you got the loop to have a different chain ID.  At  
this point, to change the chain ID of those residues, you would need  
to write out the PDB file (File... Save PDB) and text-edit it.  Be  
careful not to make multiple residues with the same number and chain  
ID (i.e. there should not be two residues that are both number 30 in  
chain A). Editing could be done manually in a text editor, or it may  
be possible with one of these PDB-file-editing Web servers:
<http://www.igs.cnrs-mrs.fr/Caspr2/magicPDB.cgi>
<http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/inputpage.html>

The other way to build peptides in Chimera is with Build Structure  
(under Tools... Structure Editing), Add Atoms section, peptide  
sequence option.  That builds peptides that are not connected to your  
existing structure, but you can enter whatever chain ID you want in  
the dialog.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html 
 >

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Apr 10, 2009, at 6:58 AM, Fajer wrote:

> Hi,
> I am a complete newbie to chimera.  I have added a loop sequences to
> using addaa but the new loop has a different chain designation from  
> the
> rest of the molecule.   "Combine" command preserved the differences in
> chain id.  How can I make the new loop chain to be the same id as  
> the host ?
> peter