From: Axel Kohlmeyer (
Date: Mon May 15 2006 - 04:52:05 CDT

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.


AM> Thank you very much in advance
AM> Best wishes

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.