VMD-L Mailing List

From: Stefan Doerr (stefdoerr_at_gmail.com)
Date: Fri Apr 22 2016 - 04:34:16 CDT

Ok, that settles it then. I will use C, CA, N, O instead of backbone.
Thanks Ashar :)

On Fri, Apr 22, 2016 at 11:32 AM, Ashar Malik <asharjm_at_gmail.com> wrote:

> 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
>