VMD-L Mailing List

From: Casey Johnson (j.casey.johnson_at_gmail.com)
Date: Sat Aug 27 2011 - 09:24:07 CDT

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.

Thank you for your help,
Casey