VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Fri Apr 24 2020 - 11:49:33 CDT

Extensions > Visualization > Color Scale Bar

The menu that appears should list color scale options.

On Sat, Apr 25, 2020 at 12:24 AM Aiswarya Pawar <aiswarya.pawar_at_gmail.com>
wrote:

> 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
>>
> 

-- 
Best,
/A