VMD-L Mailing List

From: Melquiond (adrien.melquiond_at_ibpc.fr)
Date: Mon Jul 17 2006 - 09:23:03 CDT

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>