VMD-L Mailing List

From: Mark Harder (harderm_at_onid.orst.edu)
Date: Wed Jul 19 2006 - 21:09:08 CDT

 
 (Perhaps I sent this to the wrong address. I've gotten no feedback about
it.)-MH, Wed. 7/19/06
 
 
> -----Original Message-----
> From: Mark Harder [mailto:harderm_at_onid.orst.edu]
> Sent: Monday, July 17, 2006 4:00 PM
> To: 'owner-vmd-l_at_ks.uiuc.edu'
> Subject: RE: vmd-l digest V1 #579
>
> This isn't any kind of solution; but it reminds me of a strange
> behavior of v. 1.8.4 on WinXP, sp2. I was looking at a homodimeric
> receptor taken from the PDB. It had identical ligands bound to both
> monomers, and I only wanted to display the ligand bound to the A chain,
> since I was hiding the B chain. I was using the Bond representation.
> First I tried selecting by atoms index, which was bizarre. Most displayed
> bonds were from the A chain, but a few belonged to the ligand in the B
> chain. I visually inspected the atom coordinates, and the 2 sets seemed
> to be well-separated, not scrambled. Eventually, I realized that the pdb
> file also assigned the 2 ligands as residues with different indices -- 500
> and 1500. When I selected residue index 500, only the bonds in the A
> chain were displayed, as desired!
> Does anyone know what's going on here? It's not urgent of course.
> Just for future reference, and curiosity.
>
> Mark Harder
> Dept. Biochem. & Biophys.
> Oregon State University
> harderm_at_onid.orst.edu
 


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