From: Axel Kohlmeyer (
Date: Tue Jan 31 2012 - 07:22:44 CST

On Tue, Jan 31, 2012 at 4:04 AM, thereal sisterdot
<> wrote:
> Dear all,
> a total newby question:

...and - unfortunately - almost impossible to answer.

can you please be more specific and descriptive in
what you are doing, how to reproduce the behavior
and what step exactly is not working?

with the kind of broad descriptions and shortcut
notation of what you are doing, it is difficult to
reproduce it and understand what your problem is.


> i am trying to use structural alignment tools as provided in the pdb
> workbench.
> 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)"
> or
> "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!
> best
> Maria

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.