VMD-L Mailing List

From: Shyam Saladi (saladi1_at_illinois.edu)
Date: Wed May 07 2014 - 00:45:46 CDT

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:
https://www.dropbox.com/s/6646mv1yakwj6ou/sidechains.png

view with Calpha's: 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 (sequence VYEKRRTA -- doesnt work) but
splitting it up into two does work (sequence 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