VMD-L Mailing List

From: Raag Saluja (saluja.raag_at_gmail.com)
Date: Mon Oct 29 2018 - 03:48:21 CDT

You’re right. Your command (resid 1 to 50 and protein and chain A) works
perfect with the pdb file downloaded from protein data bank. However, I was
trying to do the same with a pdb file obtained after simulating the protein
(I simulated it using gromacs and converted the final gro file into pdb),
but in vain. How do you suggest I go about this, please?

On Mon, 29 Oct 2018 at 1:24 PM, amin sagar <aamin.sagar_at_gmail.com> wrote:

> Just to check, are you sure your chain name is A? Otherwise it should be
> replaced with the name of the chain you would like to select.
>
> On Mon, 29 Oct 2018 at 8:51 AM, Raag Saluja <saluja.raag_at_gmail.com> wrote:
>
>> Thank you for your prompt replies! I tried both resid 1 to 50 and chain
>> A; and resid 1 to 50 and protein and chain A. Neither worked! The selected
>> area just got deselected.
>>
>> On Mon, 29 Oct 2018 at 1:17 PM, amin sagar <aamin.sagar_at_gmail.com> wrote:
>>
>>> Hi. Something like
>>>
>>> protein and chain A and resid 1 to 50
>>>
>>> should work.
>>>
>>> Amin.
>>>
>>> On Mon, 29 Oct 2018 at 8:38 AM, Raag Saluja <saluja.raag_at_gmail.com>
>>> wrote:
>>>
>>>> Hi!
>>>>
>>>> I am working on a heterodimer. I wanted to highlight certain residues
>>>> and keep the rest of the protein translucent. So I did create rep and then
>>>> selected the residues by giving the command "(resid 1 to 50) and
>>>> (protein)".
>>>> However, this selects the first 50 residues in both the chains. What do
>>>> I do so that only the first 50 residues are selected, be they in the first
>>>> or the second chain
>>>> (and not 50 each of both the chains)?
>>>>
>>>> Thank you in advance!
>>>> Regards,
>>>> Raag
>>>>
>>>