VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Fri Apr 24 2020 - 08:37:53 CDT

A .pdb file is a .pdb file. The format doesn't change, so you can still use
a beta or occupancy column to store a value. You'd need to do something
like this:

#Read in your data
set fin [open file.dat]
while { ! [eof $fin] } {
#This should get you your resid and contactnum in a list
set input [split [gets $fin]]
set resid [lindex $input 0]
set contactnum [lindex $input 1]
set sel [atomselect top "resid $resid"]
$sel set beta $contactnum
$sel delete
}
#close the file
close $fin

-Josh

On Fri, Apr 24, 2020 at 2:21 AM Aiswarya Pawar <aiswarya.pawar_at_gmail.com>
wrote:

> 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
>>>
>>