VMD-L Mailing List

From: Aiswarya Pawar (aiswarya.pawar_at_gmail.com)
Date: Fri Apr 24 2020 - 02:47:37 CDT

Hi,

Thanks for your quick response.
Actually that works for atomistic type pdb, I wanted to know how do i work
out for a coarse grain pdb file
which doesnt have a B-factor column.

On Fri, Apr 24, 2020 at 1:51 AM Ashar Malik <asharjm_at_gmail.com> wrote:

> The pdb atom record allows for a temperature factor value. I think column
> 61 through 66.
>
>
> For each residue that has contacts assign a value to that residue's in the
> temp-factor.
>
> Then load the new protein structure and use the representation to colour
> by temp - factor.
>
>
> This will automatically light up residue's with values other than 0 and
> scale colours accordingly.
>
>
> On Fri, 24 Apr 2020, 2:17 PM Aiswarya Pawar, <aiswarya.pawar_at_gmail.com>
> wrote:
>
>> Dear All,
>>
>> I have coarse grain simulation of protein and ligand contact data, ie a
>> dat file which has residue number in column1 and number of contacts of
>> ligand to protein in column2. I want to map these contact intensity onto
>> the protein structure ie pdb structure using VMD. How do i plot the color
>> scale contacts onto the structure. Can anyone help with this.
>>
>> Thanks
>>
>