VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 20 2013 - 17:31:17 CST

Hi,
  I would suggest that you try using the VMD merge structures plugin,
psfgen, or something similar to build the assembly rather than concatenating
files. That said, if you've not had any luck solving this already,
I would guess that you would have better results if you loaded them
into VMD as separate molecules, wrote them out to new files with unique
chain IDs, and then concatenated those files, so that VMD isn't trying to
treat them all as one chain. If, on the other hand, you're trying to
merge them into a single chain, then I think we'd have to see the details
of your file to determine what's going wrong there.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Dec 01, 2013 at 01:22:27AM +0000, Andy Lam wrote:
> Hi,
> I concatenated 4 chains of an assemble manually by pasting one after
> another with a text editor and had the END removed. However, the resulting
> pdb could only be viewed intact with representations - lines/bonds/vdw -
> but a part of one chain (always the same part of one chain) was missing in
> - ribbon/cartoon - form. I wonder how this problem may be solved, since
> the concatenated pdb looked fine in the forms of lines/bonds/vdw.
> Thanks
> Andy 

-- 
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
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