If you want to see the bonds, perhaps those programs have a
bondbydistance cmd like leap's? Or a way of providing a template, e.g.
in the form of a pdb with CONECT records.
Bill
On 5/13/19 12:46 AM, Saikat Dutta chowdhury wrote:
> Thank you for your reply.
> I have used both pymol and vmd for viewing the molecule.
>
> with regards,
> Saikat
>
> On Sun, May 12, 2019 at 2:23 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> On 5/11/19 11:40 PM, Saikat Dutta chowdhury wrote:
>>> 1. When I am opening the pdb files for the system I found out that the
>>> phosphate moieties are no longer attached to the amino acids.
>> What viewer? Likely it's seeing a residue it doesn't know the bonding
>> of, since it's an unknown res name.
>>
>> Bill
>>
>>
>>
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Received on Mon May 13 2019 - 01:00:02 PDT
