VMD-L Mailing List

From: Aiswarya Pawar (aiswarya.pawar_at_gmail.com)
Date: Fri Apr 24 2020 - 11:23:53 CDT

Hi Ashar,

It worked perfectly. Thank you so much. I have one more doubt, how do you
add an colorscale to the snapshot and also how can I give a customised
colorscale.

Thanks

On Fri 24 Apr, 2020, 2:27 PM Ashar Malik, <asharjm_at_gmail.com> wrote:

> A standard PDB file, will have the correct number of columns.
> Even if nothing is indicated inside those columns, i.e. they are empty -
> they are still part of the PDB ATOM RECORD - even if the atoms are coarse
> grained residues.
> The answer I gave previously is still valid.
>
> Either manually or trough a script - open up the coarse grained PDB file
> -- against each coarse grained residue add the number of contacts in the
> occupancy or b-factor column.
>
>
> On Fri, Apr 24, 2020 at 3:47 PM 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
>>>>
>>>
>
> --
> Best,
> /A
>