VMD-L Mailing List

From: Sarah Richards (sarahrichards57_at_gmail.com)
Date: Fri Jul 06 2012 - 08:16:04 CDT

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 (http://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py/) 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