VMD-L Mailing List

From: MannyEful E (mannyeful_at_gmail.com)
Date: Wed Nov 19 2014 - 08:18:25 CST

Hahaha.

Hello Kshatresh,

1) Are you trying to show only your region of interest?
2) Or are you trying to update the frames for only your region of interest
and freeze the others??
3) Or maybe you're trying to make the molecules whole so that they don't
split across the box?

For 1.
Go to the graphics representation menu and make a selection for your region
of interest. (graphics > representations)
In the trajectory tab, tick update each frame.

For 2.
For the second one I have an idea, but am not so sure if it's feasible.
Maybe you could make a representation for your selection, one for each
frame. And then loop through a script to show and hide the representations.
For instance: (atomselect top "within 5 of resname LYR" frame 23)
With: (atomselect top "not within 5 of resname LYR" frame 1)
Example of rep looping:
http://www.ks.uiuc.edu/Research/vmd/vmd-1.6.1/ug/node177.html
Example of fading: http://www.ks.uiuc.edu/Research/vmd/workshop/movie.html

For 3.
I think it has something to do with pbc wrap or whole options. If I recall
correctly, one of these options are irreversible once they have been made
whole.
For example: http://lammps.sandia.gov/threads/msg42801.html

I hope this helps!

END

On Wed, Nov 19, 2014 at 12:54 PM, Ashar Malik <asharjm_at_gmail.com> wrote:

> Hey,
>
> You should try putting a bucket under the monitor, otherwise you will
> create a mess :D
>
> Sorry couldn't resist ...
>
> What you are looking for is
>
> Extension > Analysis > RMSD trajectory tool > Align.
>
> Unless you are looking for more than this.
>
> Best,
> /A
>
>
>
> On Thu, Nov 20, 2014 at 1:09 AM, Kshatresh Dutta Dubey <
> kshatresh_at_gmail.com> wrote:
>
>> Dear Users,
>>
>> Is there any way to fix the movement of whole complex during trajectory
>> visualization so that I can focus on the movement of particular region of
>> the system. During visualization of trajectories sometime complex goes out
>> of the monitor.
>>
>> Thanks in advance
>> Regards
>> Kshatresh
>>
>>
>
>
> --
> Best,
> /A
>