VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 05 2018 - 15:12:20 CDT

Kelly,
  The behavior you observe is the default behavior when VMD gets a
concatenated PDB file. I'm not familiar with the details of the tutorial
you're working, but I can say that this is definitely what the VMD
PDB plugin does if you concatenate multiple PDBs together presently.
That said, you can show the four monomers at once using the draw-multiple-frames
controls in the trajectory tab, by listing the frame range 0:3 or similar...

Best,
  John

On Thu, Jul 05, 2018 at 03:24:41PM +0000, McGuire, Kelly wrote:
> I am going through the membrane/protein tutorial, and after I get through
> the Building The Tetramer step (for my protein 5TTC, not KcsA), I open the
> structure in VMD and VMD thinks the 4 monomers are 4 different frames
> instead of 1 tetrameric structure. What would cause VMD to open my
> concatenated pdb file with the monomers as frames instead of a single
> structure?
>
> Kelly L. McGuire
>
> PhD Scholar
>
> Department of Physiology and Developmental Biology
>
> Brigham Young University
>
> LSB 3050
>
> Provo, UT 84602 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/