From: Anna Modzelewska (
Date: Tue Jan 10 2006 - 10:29:43 CST

I have problem with STRIDE. In my model I have two proteins and a ligand. When I load the whole model into the VMD it doesn't recognize the secondary structure. However when I load the proteins and the ligand as two separate files it does. The same behavior I observed in the model containing 5 proteins, and ATP. It's strange because STRIDE recognize the sec. str. even when protein has non-standard residues for which I had to define the topology by myself. Once it finds in the pdb file a residue that is not a part of protein or membrane it doesn't do anything.
It's not funny to cut the files and load them separately each time when I need to see the secondary structure or to use the new-cartoon graphic representation.
Is there any way to resolve this problem?

Thanks for any advises

 Anna Modzelewska, M.Sc.
 International Institute of Molecular and Cell Biology
 Trojdena 4, 02-109 Warsaw, Poland
 phone: +48 22 5970721 fax: +48 22 5970715