You'll need to submit an example of the problem in a chimera bug report for a definitive answer. But off the top of my head, the reason why VMD shows the output of NAMD better is that they are developed by the same group. And the reason why Chimera doesn't show it as well is probably because Chimera is following the PDB standard and VMD/NAMD isn't :-). Or possibly the NAMD generated PDB files are underspecified and VMD knows how to compensate. Who knows without an example? - Greg On Sat, 6 Feb 2010, Keith Battle wrote:
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.
Best,
Keith Battle Research Technician University of South Alabama