VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 16 2014 - 14:36:08 CDT

Hi,
  Sorry for the slow response, I've been traveling for several weeks.
Do you have a PDB or other structure file that contains this structure
along with a VMD saved state that I can use to load and display it in the
way you've shown in the images you provided? If you could post those files
as well, that'd be very helpful.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, May 07, 2014 at 12:45:46AM -0500, Shyam Saladi wrote:
> Hello,
> I am rendering a protein structure with VMD and am encountering difficulty
> in having my structure render correctly.
> In two chains of the four in my structure using NewRibbons, VMD doesn't
> connect two adjacent residues, but instead has the ribbon following the
> side chain of one (ARG) and stops at the Calpha of the other (LYS):
> view showing
> sidechains:A https://www.dropbox.com/s/6646mv1yakwj6ou/sidechains.png
> view with
> Calpha's:A https://www.dropbox.com/s/u5c5gf19xyv9daq/CA_image.png
> I would somehow like to correct this so the ribbon to follows the protein
> sequence. In case it's useful, when I try an atomselect of the contiguous
> sequence, VMD is unable to find it (sequenceA VYEKRRTA -- doesnt work) but
> splitting it up into two does work (sequenceA VYEK or sequence RRTA). On
> the other hand, the sequence viewer extension does list them in the
> expected order.
> Could anyone offer any insight or assistance? I appreciate the help in
> advance.
> Thanks,
> Shyam 

-- 
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/