[Chimera-users] Chimera/VMD visualization difference

Keith Battle keith.battle at gmail.com
Sat Feb 6 06:25:43 PST 2010

Hello Chimera team,


I recently conducted a MD simulation of a 12-mer peptide adjacent to a
hydroxyapatite crystal using NAMD 2.6. When I viewed the output coordinates
from the simulation in pdb format using Chimera 1.4, the protein ribbon was
broken and the hydrogens of certain residues were not bonded but in close
proximity. All of the non-bonded hydrogens were colored purple by default.
The waters of the system and the crystal looked normal. Overall, the protein
looked distorted. I decided to visualize the peptide using VMD 1.8.7 and to
my surprise the protein ribbon was intact with all hydrogens bonded to their
respective residues. Any insight into why this difference occurred would be
greatly appreciated.




Keith Battle

Research Technician

University of South Alabama 

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