VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jul 17 2006 - 10:40:43 CDT

Hi,
  It looks to me like you're missing a few bonds, which is causing
the cartoon representation to do odd things. When loading files from
the PDB format, VMD uses a distance-based bond search, and you've got
a few that are far enough away that they're not making the cut. This
is the reason for the odd looking cartoon rep, it's as if you chopped
up your protein into sections. You could either specify bonds with
CONECT records, make a PSF or other file with this information, or something
along those lines.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jul 17, 2006 at 04:23:03PM +0200, Melquiond wrote:
> Dear VMD users,
>
> First of all, I want to thank Axel for his reply, even if my thanks are a
> little bit late ... Indeed, the NewCartoon representation solved my former
> problem and I have updated my VMD version now !!! I hope that you don't hold
> this lateness against me and that you'll have a look at my new
> problem ;-) !!!
>
> So, that's the snag ! In attachment, I join you a PDB file generated by a
> personal program. If you display this structure with the NewCartoon
> representation, then you will see that two strands are "not very well" ended,
> with a circular shape for the edge arrow ... I don't understand this bug and
> I suspect my PDB file but all is ok with the Cartoon representation ... I
> will be grateful for any comment ...
>
> platform : linux i386 32-bit
> vmd version : vmd-1.8.4
>
> --
> Adrien
>
> -------------------------------------------------------
> Adrien Melquiond, PhD student
> Laboratoire de Biochimie Theorique, CNRS UPR 9080, IBPC
> 13, rue Pierre et Marie Curie, 75005 Paris - FRANCE -
>
> Tel : +33 [0]1 58 41 51 63
> Fax : +33 [0]1 58 41 50 26
> Email : adrien.melquiond_at_ibpc.fr
> www : http://www.ibpc.fr/~melquion
> -------------------------------------------------------
>
> > On Sun, 14 May 2006, Melquiond wrote:
> >
> > AM> Dear VMD users,
> >
> > dear adrien,
> >
> > AM> I've searched for a moment before to submit my problem to the mailing
> > list and AM> I hope the reason isn't too naive. Between the output of
> > STRIDE used directly AM> and the assignment operated by STRIDE in VMD, I've
> > got some differences !
> >
> > when reporting this kind of problems, please always state what version
> > of VMD you are referring to and what platform you are running on.
> > also, please describe how to reproduce your problem.
> >
> > AM> For instance, I attached a PDB file that illustrate very well this
> > difference AM> (STRIDE output assigns 4 beta strands and only two of these
> > are represented AM> under VMD). I specify that we use a coarse-grained
> > protein representation and AM> that the name of the beads representing the
> > side-chains aren't usuals. I said AM> that because a previous message made
> > mention of a problem encountered with AM> STRIDE when the PDB file
> > countains some unsuals residues. M. John Stone wrote AM> that "STRIDE is
> > fed it's data directly from VMD, not from the original file" AM> and I
> > wondered if this cannot be the cause of my problem ...
> >
> > no. actually i could see all four beta strands with both VMD version
> > 1.8.3 and VMD version 1.8.4 when using the NewCartoon representation.
> > i assume, that you must be using the Cartoon representation, which
> > indeed does show only two beta sheets, due to the fact that two of
> > them are too short. this it is a known limitation of that
> > representation. please let us know if NewCartoon works for you, too.
> >
> > salut,
> > axel.
> >
> > AM>
> > AM> Thank you very much in advance
> > AM>
> > AM> Best wishes
> > AM>
> > AM> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078