From: John Stone (
Date: Thu Jul 12 2012 - 10:24:08 CDT

  I believe the problem you're having is related to the chain name issue
you mentioned below. If I'm not mistaken, (I haven't had to look at the
STRIDE code for years, so this was after a quick reading of the code)
I believe VMD is writing a STRIDE input PDB file that doesn't reproduce
the original segment name or chain field as the chain field in the input PDB,
and this may be the reason for the behavior you see.
I would be curious to know why STRIDE decides to behave differently based on
whether the strands have the same chains or not.

  John Stone

On Fri, Jul 06, 2012 at 09:16:04AM -0400, Sarah Richards wrote:
> Hello VMD users and developers,
> I am having a problem getting the correct secondary structure to show for a beta-sheet in VMD. I have arranged the beta-strands parallel and positioned the strands to allow for the correct hydrogen bonding. When I show the secondary structure in Representations, however, it does not show the yellow arrows for beta-sheet. When I built each strand (in MOE), I set the dihedrals for a parallel beta-sheet and I have double-checked that these are correct.
> I have previously built a beta-sheet with an antiparallel arrangement, and VMD displayed the correct beta-sheet secondary structure.
> I checked the secondary structure of the parallel beta-sheet in the Stride web interface ( and found that the beta-sheet conformation is only shown when each strand has a different chain name. When I load this PDB in VMD, however, beta-sheet secondary structure is not shown. I have attached a PDB with a different chain name for each strand.
> I am using a VMD 1.9 for Mac (running Lion). I would greatly appreciate any help.
> Thank you,
> Sarah Richards

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