From: John Stone (
Date: Thu Sep 01 2011 - 07:59:26 CDT

  I think this is most easily answered by looking at the STRIDE
source code. I would expect that it is looking for the exact
atom names used in the PDB, rather than the more generic
atom names that you listed below. I'd suggest grepping for
"CA" etc in the STRIDE source code and see what you find there.
We didn't write STRIDE, so I don't otherwise know the answer
off the top of my head.

  John Stone

On Wed, Aug 31, 2011 at 10:08:11AM -0400, Casey Johnson wrote:
> Hi Users,
> I have a custom peptide that I'm trying to represent as a ribbon, however,
> the molecule disappears when I select ribbon. I'm guessing there is
> something weird about my .pdb file. What information is needed in the
> .pdb file for the STRIDE algorithm to properly calculate the structure?
> Is there a certain naming convention that I should be using? Currently
> the peptide nitrogen is named 'N', the hydrogen is 'H', the alpha carbon
> is 'CA', the carbonyl carbon is 'C' and the carbonyl oxygen is 'O'. I
> looked through the archives but was unable to find anything but I
> apologize if a similar question has been posted.
> I've attached the pdb file I'm using for my simulation.
> Thank you for your help,
> Casey

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