[Chimera-users] PDB morphing

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 28 15:50:18 PDT 2008

Hi Matt,
At least in my smaller-scale tests, it worked to morph multiple chains  
in one model to multiple chains in another model.  What I tried:

(a) Lin-7/Lin-2:  PDB 1zl8 is an NMR structure with A and B chains.   
It contains multiple models delimited with MODEL/ENDMDL records.  I  
tried morphing from the first to the second to the third model and  
confirmed that both A and B chains morphed.

(b) insulin:  PDB 1aph has A and B chains, PDB 1fub has A-D, where  
either A,B or C,D could be paired with the first structure.
I opened 1aph, opened 1fub and deleted its C,D chains - then morphing  
worked.  Then to confirm different chain IDs are OK, I closed and  
reopened 1fub, then deleted its A,B chains - again morphing worked.

(c) antibody Fab fragment:  since insulin's A and B chains are  
disulfide-linked, I wanted to try another example where the chains  
aren't covalently bonded, just in case.  PDB 1kem has L,H chains while  
PDB 1mh5 has L,H but another set A,B.  I deleted L,H from 1mh5 and  
confirmed that it did work to morph between the two structures and  
that both chains moved.

I believe that atom and residue numbering are not used at all and have  
morphed between many structures with different numbering, such as  
homologous proteins with fairly low percent identity.

In your agglomerated files, I believe that although the chain IDs do  
not need to match between conformation 1 and conformation 2, the chain  
IDs should be unique in each file.  That is, no file should contain  
more than one chain with the same ID.  Other than that, I don't have  
ideas of what could be amiss with your input.

Do you get any messages from Chimera, or does it happily go about its  
business of  not generating what you want?
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

P.S.  I was using last night's build, but I believe there have not  
been any changes in Morph Conformations for several weeks (should be  
identical to the last production release).

On Jul 28, 2008, at 9:39 AM, Dougherty, Matthew T. wrote:

> we tried the one file approach, did not work out.
> will try again.  does it make any difference about the chain id or  
> atom number?
> Matthew Dougherty
> 713-433-3849
> National Center for Macromolecular Imaging
> Baylor College of Medicine/Houston Texas USA
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