VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 29 2016 - 21:53:46 CDT

Hi,
  When you load the structure, VMD will print out how many protein
fragments it finds. If VMD is unable to identify your chains as
protein fragments, e.g. due to unrecognized atom or residue names,
then the various cartoon representations will not work because
they specifically target protein fragments. The nomenclature VMD
is expecting for the proteins is derived from protein data bank
atom and residue naming conventions, so if Modeler did something
else, that would explain the issue. If you read the mailing list
archive and/or tutorials you will find that you can rename atoms quite
easily, and then cause VMD to reanalyze the structure, and to save out
new structure files if necessary.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Apr 30, 2016 at 08:04:47AM +0530, surendra jain wrote:
> Hi,
> There were some residues missing in the protein that I use for my
> study. I did a homology modeling and added the missing residues using
> Modeler. I can view my final protein structure using lines and bonds
> in VMD. But I cannot view the full protein in cartoon, trace or tube
> format ( only 2 chains out of 4 chains are visible).
>
> Any help will be appreciated.
>
> Best Regards,
> Surendra 

-- 
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/