[Chimera-users] PDB morphing

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 28 09:37:01 PDT 2008

Hi Matt,
Currently each input conformation for morphing can only be one model.   
Chimera considers each input file to be one model (or more, if the  
file contains multiple sets of coordinates delimited with MODEL/ENDMDL  

Without code change, the only way I can think of is to put each entire  
structure of 24 monomers in a single PDB file.  This may be a pain, as  
you would probably want to give each monomer a unique chain ID so that  
all residues in the "model" are still uniquely identifiable by residue  
number/chain ID.  Then you would have one file per conformation.

Since I haven't actually tried this, I recommend trying on a subset of  
2-3 chains before going to all the trouble of putting all 24 in a  
file!  Maybe the others can come up with a more elegant solution.
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

On Jul 27, 2008, at 8:13 PM, Dougherty, Matthew T. wrote:

> I have a complex structure in two conformations: resting and active.
> Each structure consists of 24 monomers, corresponding to 24 pdb files.
> Each monomer file between conformations matches in terms of atom  
> numbers, chain ID, etc.
> I can morph a single monomer between conformations.
> I am having no success morphing all the monomers simultaneously  
> between the conformations.
> Any suggestions on how to organize my data to overcome this?
> thanks, Matt

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