VMD-L Mailing List

From: Christoph Weber (weber_at_scripps.edu)
Date: Thu Jul 20 2006 - 17:19:08 CDT

It would help to know the PDB ID of your receptor structure to check
this out.

However, looking inside the actual PDB file and trying to identify
unique features of the part you are interested in _is_ the general
solution to your problem, as you found out. Quite often a
visualization program alone cannot give you enough information, or at
least not quickly enough.

Christoph

Mark Harder wrote:
> (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 

-- 
|  Dr. Christoph Weber              Sen. Applications Specialist
|  Research Computing, TPC21        858-784-9869 (phone)
|  The Scripps Research Institute   858-784-9301 (FAX)
|  La Jolla  CA  92037-1027         weber_at_scripps.edu
|  http://www.scripps.edu/~weber/
Everything's got a moral, if only you can find it.
-- Lewis Carrol, Alice in Wonderland