VMD-L Mailing List

From: Samuel Bowerman (sbowerma+namd-l_at_hawk.iit.edu)
Date: Thu Apr 21 2016 - 13:45:53 CDT

Hi Stefan,

I am not a VMD developer, but my best guess would be that VMD isn't sure
whether PTR is protein or nucleic, so it may be selecting both sets of
"backbones" (protein = C,CA,N,O ; nucleic = O5', C5', C4', C3', O3', P,
OP1, OP2). So the backbone selection isn't "failing", but it is a bug
originating from the fact that your residue "type" is ambiguous.

Take care,
Sam

On Thu, Apr 21, 2016 at 11:27 AM, Stefan Doerr <stefdoerr_at_gmail.com> wrote:

> Hi, I was trying to remove a engineered residue from a protein when I fell
> upon weird behaviour in atomselect.
> http://www.rcsb.org/pdb/explore.do?structureId=5HX8
>
> If you try "resname PTR and backbone" you will notice that this leaves
> behind 3 atoms, P, OP1 and OP2 which are obviously not backbone.
>
> What is the reason for that?
>
> Greetings,
> Stefan
>