From: Ashar Malik (asharjm_at_gmail.com)
Date: Fri Apr 22 2016 - 04:32:13 CDT

Please refer to page 82 -- Table 6.5 of the user guide here:
http://web.mit.edu/vmd_v1.9.1/ug.pdf

On Fri, Apr 22, 2016 at 9:05 PM, Stefan Doerr <stefdoerr_at_gmail.com> wrote:

> 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
>>>
>>
>>
>

-- 
Best,
/A