VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 02 2016 - 10:57:03 CDT

Hi,
  I looked at this visually the other night but did not manage
to find an obvious explanation. Unless I missed something that
someone else happens to catch, I may have to dig into the code to
figure out why the other two protein chains are not being recognized
as protein. While I didn't see anything when looking, I'm guessing that
the problem has to do with an unusual bond topology somewhere or
unexpected atom types in the residues at the start/end of the affected chains.
My time is extremely limited for the next three weeks, so
I can't promise anything until later this month. Someone else might
be able to catch this in the mean time if they have a close look.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Apr 30, 2016 at 09:52:26AM +0530, surendra jain wrote:
> Hi John,
>
> many thanks for your message. I get the following message from VMD
>
> Info) Atoms: 11656
> Info) Bonds: 12005
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 1503
> Info) Waters: 0
> Info) Segments: 4
> Info) Fragments: 4 Protein: 2 Nucleic: 0
>
> I have 4 protein chains, but it can identify only 2 of those. I am
> attaching the full protein structure.
>
> Kindly check what is the problem.
>
> Best Regards,
> Surendra
>
> On 4/30/16, John Stone <johns_at_ks.uiuc.edu> wrote:
> > 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/
> > 

-- 
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/