From: Matthew Thomas Geballe (
Date: Tue Dec 07 2004 - 20:43:11 CST


Thanks for your quick reply. It is interesting that if the only atoms in
the pdb file are CA atoms and each residue only has a CA atom then the
tube representation works if the selected text is "all". If I change the
selected text to "protein" the tube disappears. However when I have some
residues with CAs only and some with the entire residue only the backbone
of the complete residues are displayed when I choose tube representation
with selection "all". Somehow a tube representation can be created out of
non-protein CAs if they are all that is present, but if there is a
nonempty "protein" group then the others don't get displayed. Do you know
of any way to modify this?

Thanks for your time,


On Tue, 7 Dec 2004, Andrew Dalke wrote:

> Hi Matthew,
> > I have a pdb structure that is mostly alpha carbons except for a few
> > residues around a ligand. I would like to display the entire protein
> > with a CA tube and the active site in a more detailed representation.
> > However it seems that the residues that are only CAs are not
> > recognized as part of the "protein" keyword. When a pdb file is only
> > CAs the residues are recognized as protein. Is there any way to
> > circumvent this feature and draw a tube representation for all the CA
> > atoms? Can I adjust what is included in the "protein" keywords?
> I wrote that code about ... a decade ago now (!).
> Unless things have changed more than I thought in the last 6 years
> since I last worked on VMD, the fundamental problem is in how a
> "protein" structure is determined.
> The code I wrote says a residue is a protein residue if it has
> atoms named N, C, CA, and O (or OT1/OT2 for terminals). If there
> are only C-alphas then that detection doesn't work. I don't recall
> now if those atoms need to be covalently bonded; I don't think so.
> A more sophisticated algorithm could just look for the C-alpha
> atoms and piece together the protein that way. There are some
> complications because of different interpretations of the PDB
> format.
> If it happens there are many problems downstream. For example
> the ribbon drawing code assumes all protein chains have all four
> peptide atoms. It uses the angles to figure out the ribbon
> orientation.
> These can be fixed but so far no one's needed enough to actually
> do it.
> Andrew

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