[Chimera-users] Chimera/VMD visualization difference

Eric Pettersen pett at cgl.ucsf.edu
Mon Feb 8 14:16:27 PST 2010

On Feb 6, 2010, at 6:25 AM, 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.

Hi Keith,
	Assuming we're talking about the PDB file you attached to Trac ticket  
#8165, then I guess I'm puzzled.  Chimera 1.4 displays it correctly  
AFAICT.  Certainly all the hydrogens are bonded.  I've attached two  
images of the peptide, one without ribbons and one with.  Some of the  
side chains of the one with ribbons look a little weird because the  
carbon alpha position is interpolated to lie on the ribbon which can  
produce a weird looking CA-CB bond (and N-CD bond in the case of  
	Now, the PDB file does have problems.  NAMD has put a lot of garbage  
in the 'element' column of the ATOM/HETATM records (last column on the  
right).  All the calciums in your crystal have element 'C' instead of  
'CA' and some (but not all) of the hydrogens in your protein are  
'LP' (lone pair) instead of 'H'.  Chimera honors the former  
unfortunately but knows that the latter is garbage and falls back to  
guessing the element from the atom name and correctly deduces that  
it's hydrogen.
	From your description it sounds like that -- for you -- Chimera is in  
fact getting the element type wrong for those hydrogens and possibly  
other atoms as well.  Are you really opening precisely the file you  
attached in the 1.4 version of Chimera?  If you're certain that that's  
the case, try labeling the disconnected atoms with their element types  
(Actions->Label->element) and let me know what they are.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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