VMD-L Mailing List
From: Shyam Saladi (saladi1_at_illinois.edu)
Date: Fri May 16 2014 - 15:47:59 CDT
Thanks for your email! Fortunately, Javier Baylon suggested in another
conversation off the mailing list that I load both the psf and pdb files,
not just the pdb file.
I generated the psf file using psfgen and then loaded both. I'm not
entirely sure why, but this solved the issue.
On Fri, May 16, 2014 at 2:36 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> 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.
> John Stone
> 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
> > in having my structure render correctly.
> > In two chains of the four in my structure using NewRibbons, VMD
> > connect two adjacent residues, but instead has the ribbon following
> > 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
> > sequence. In case it's useful, when I try an atomselect of the
> > sequence, VMD is unable to find it (sequenceA VYEKRRTA -- doesnt
> work) but
> > splitting it up into two does work (sequenceA VYEK or sequence RRTA).
> > 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