VMD-L Mailing List

From: Stefan Doerr (stefdoerr_at_gmail.com)
Date: Fri Apr 22 2016 - 04:05:10 CDT

Ohhh I see. There is no way to get only protein backbone though, right?
Because if I do "resname PTR and protein and backbone" it still gives the
same atoms since they are part of the protein...
I guess I could do "resname PTR and name C CA N O" but is it general enough
across various forcefields and naming conventions? Does anyone know what
"backbone" exactly translates to under the hood?

On Thu, Apr 21, 2016 at 8:45 PM, Samuel Bowerman <
sbowerma+namd-l_at_hawk.iit.edu> wrote:

> 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
>>
>
>