VMD-L Mailing List

From: Andrew Dalke (dalke_at_dalkescientific.com)
Date: Tue Dec 07 2004 - 19:46:58 CST

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
                                        dalke_at_dalkescientific.com