From: thereal sisterdot (
Date: Tue Jan 31 2012 - 03:04:52 CST

Dear all,

a total newby question:

i am trying to use structural alignment tools as provided in the pdb

i am splitting up the models into separate pdb files and loading them as
new molecules into vmd.
in vmd: when using the vmd_calculate_structure i typically get two types of
error messages:

"Residue ....- is involved in 6 hydrogen bonds (5 are allowed)"
"No hydrogen bonds found"

depending on the tool.

any recommendations on how to visualize the structural alignments?
particular cartoon/ribbon modes are no good with the errors in stride?
do i need to use other 3d viewers- eg pymol?

thanks for any advice!