[Chimera-users] Morph structure with ligands.

[Elaine Meng]

Hi Hernando,
As I had understood it (and had written in the documentation)
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#pairing>:

"HET residues such as ligands and ions are only included if they are present in both structures and attached to the same atom(s) in the paired chains by at least one “covalent” bond (which can be an unrealistic bond added manually, e.g., with the command bond, and subsequently undisplayed) or ion coordination pseudobond. 

Once residues are paired, atoms in common within those residues are paired. In paired residues of the same type, atom pairing is straightforward. In paired residues of different types, only atoms with the same names are paired, and only a single connected fragment is kept per residue.”

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco



> On Jul 11, 2017, at 8:44 AM, Hernando J Sosa <hernando.sosa at einstein.yu.edu> wrote:
> 
> Dear Chimera,
>  
>  
> When using the morphing structure tool (Tools->Structure comparison->Morph Structures) to create a movie between two structures  with ligands (HETATM)  the ligands are usually excluded from the resulting  morphed model movie. What  has to be done to keep the ligands?
> I noticed  that a morph-movie created between a structure and a copy of it  (created by making a copy in the model panel and moving the  position of the copy)  does keep the ligands, However,   in most other cases the ligands disappear, even when the ligands in the two structures have the same assigned  'residue' number in the pdb files.
>  
> Thanks
>  
> Hernando