From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Mar 26 2018 - 09:01:18 CDT

Hi Shashank, one of the best options is to use the open, puts and close Tcl
commands to write to a text file in your loop. To execute the commands in
the script, use source or play.

For more information, consult the Tcl command reference (adjust the version
number if needed):
https://www.tcl.tk/man/tcl8.5/TclCmd/contents.htm

Putting a file in the plugins folder is only needed to create a plugin: you
can do that if you wish, but you will also need to create a specific folder
for it, as well as a pkgIndex.tcl file, which will load your Tcl procedures
so that you can run them in any session.

Giacomo

On Mon, Mar 26, 2018 at 2:59 AM, Shashank Ranjan Srivastava <
sranjan_at_iiserb.ac.in> wrote:

> Hi Fiorin,
>
> Thank you for your reply and suggestion. I got distance.tcl script file
> and paste it in vmd plugin folder. With this script we can calculate the
> distance between two molecule with respect to time but I m not getting how
> to use this script in TK console directly so that I can get output file
> with plot. Could please help me regarding this.
>
> Thank You
>
> On Thu, Mar 22, 2018 at 9:01 PM, Chris Neale <candrewn_at_gmail.com> wrote:
>
>> or do a least-squared fit on the protein and then make a separate
>> selection for the lipid of interest and go to the trajectory tab and where
>> it says "now" enter "0:5:1000" to show every 5th frame from frame 0 to
>> frame 1000 (or whatever actual time selection you want)
>>
>> On Thu, Mar 22, 2018 at 9:04 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com
>> > wrote:
>>
>>> My suggestion would be to use two selections, one for the protein and
>>> one for the cholesterol molecule, compute the center of mass of each using
>>> measure center, compute the difference between the two using vecsub, and
>>> transform the three Cartesian components into whatever you like.
>>>
>>> The VMD guide has examples of custom Tcl scripts that you can look at.
>>>
>>> Giacomo
>>>
>>> On Thu, Mar 22, 2018 at 2:56 AM, Shashank Ranjan Srivastava <
>>> sranjan_at_iiserb.ac.in> wrote:
>>>
>>>> Hello Fiorin,
>>>>
>>>> In my simulation assembly I have added cholesterol molecule now I want
>>>> to see cholesterol positioning around the protein (beta barrel) with
>>>> respect to time.
>>>>
>>>> So how can I calculate change in positioning of cholesterol molecule
>>>> from geometric centre of my protein barrel and map it in two dimensional
>>>> form that how cholesterol Is moving around the barrel with respect to time.
>>>>
>>>> Thank You
>>>>
>>>> On Wed, Mar 21, 2018 at 7:36 PM, Giacomo Fiorin <
>>>> giacomo.fiorin_at_gmail.com> wrote:
>>>>
>>>>> Hi, can you explain more precisely what you are trying to do?
>>>>>
>>>>> You may find this useful if you need help with the coordinate
>>>>> transformation:
>>>>> https://en.wikipedia.org/wiki/Cylindrical_coordinate_system
>>>>>
>>>>> On Wed, Mar 21, 2018 at 2:16 AM, Shashank Ranjan Srivastava <
>>>>> sranjan_at_iiserb.ac.in> wrote:
>>>>>
>>>>>> Hello everybody,
>>>>>>
>>>>>> Can anyone please help me out regarding 2-dimensional mapping of a
>>>>>> particular lipid molecule around the geometric centre of protein molecule
>>>>>> in protein-lipid assembly.
>>>>>>
>>>>>> Thank You
>>>>>> --
>>>>>> Shashank Ranjan Srivastava
>>>>>> Molecular Biophysics Laboratory
>>>>>> Department of Biological Sciences,
>>>>>> IISER-Bhopal,
>>>>>> Madhya Pradesh
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Giacomo Fiorin
>>>>> Associate Professor of Research, Temple University, Philadelphia, PA
>>>>> Contractor, National Institutes of Health, Bethesda, MD
>>>>> http://goo.gl/Q3TBQU
>>>>> https://github.com/giacomofiorin
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Shashank Ranjan Srivastava
>>>> Molecular Biophysics Laboratory
>>>> Department of Biological Sciences,
>>>> IISER-Bhopal,
>>>> Madhya Pradesh
>>>>
>>>>
>>>
>>>
>>> --
>>> Giacomo Fiorin
>>> Associate Professor of Research, Temple University, Philadelphia, PA
>>> Contractor, National Institutes of Health, Bethesda, MD
>>> http://goo.gl/Q3TBQU
>>> https://github.com/giacomofiorin
>>>
>>
>>
>
>
> --
> Shashank Ranjan Srivastava
> Molecular Biophysics Laboratory
> Department of Biological Sciences,
> IISER-Bhopal,
> Madhya Pradesh
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin