VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Fri Apr 24 2020 - 01:51:44 CDT

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
>