[Chimera-users] Morph with Cofactors

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 6 10:15:10 PDT 2012

Hi Marco,
There have been some recent improvements, so you may want to try a daily build (if you aren't already).

Nonchain residues such as ligands, cofactors, and water molecules are only paired if the structures have exactly the same number of “het” residues with the same residue names, in the same order. The residue numbers do not have to be the same, however.

Thus you may need to delete all other het residues, often including water molecules, since generally the structures would have different numbers of waters.  If you want to display any of those deleted residues along with the morph, you could open an additional copy of either structure (but not use it to calculate the morph).

Details on how "atoms in common" between morphing inputs are identified:

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 5, 2012, at 2:16 PM, Marco Jost wrote:

> Hi,
> I am trying to morph two conformations of a protein that includes multiple cofactors. While the protein structure is morphed just fine, the cofactors are not included in the morph (or in the output PDB). I numbered the cofactors identically in both files and everything else should be consistent as well.
> Does anybody know how to include cofactors in the morphing and have them be written into the output PDB?
> Thanks!
> Marco Jost
> Ph. D. Student, Department of Chemistry
> Massachusetts Institute of Technology

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