VMD-L Mailing List

From: Melquiond (adrien.melquiond_at_ibpc.fr)
Date: Sun May 14 2006 - 15:34:43 CDT

Dear VMD users,

I've searched for a moment before to submit my problem to the mailing list and
I hope the reason isn't too naive. Between the output of STRIDE used directly
and the assignment operated by STRIDE in VMD, I've got some differences !

For instance, I attached a PDB file that illustrate very well this difference
(STRIDE output assigns 4 beta strands and only two of these are represented
under VMD). I specify that we use a coarse-grained protein representation and
that the name of the beads representing the side-chains aren't usuals. I said
that because a previous message made mention of a problem encountered with
STRIDE when the PDB file countains some unsuals residues. M. John Stone wrote
that "STRIDE is fed it's data directly from VMD, not from the original file"
and I wondered if this cannot be the cause of my problem ...

Thank you very much in advance

Best wishes 

-- 
Adrien
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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
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