[Chimera-users] centroids mutual distance etc. ?

[Elaine Meng]

Hi Marek,
If you made the centroids with “Axes/Planes/Centroids” (in menu under Tools… Structure Analysis) or command “define centroid” 
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes> 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>

...you can specify them by ID in the distance command, e.g.:
distance c1 c1
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>

 ...or measure distances using the GUI list of objects (for example, choosing two centroids in that list):
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#objectlist> 

However, if you used “measure center” with “mark true” to make the centroids, then they are just fake atoms and you can measure distances in exactly the same way as with real atoms.

I’m not aware of any (non-programming) way to make an automically updated centroid, but I think you can achieve it by creating a per-frame script in MD Movie
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>

…e.g. that deletes any pre-existing centroids (~define) and calculates a new one (define centroid…).  See the define command docs linked above for the various command options.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 27, 2014, at 4:57 PM, Marek Maly <marek.maly at ujep.cz> wrote:

> Hello,
> is there any possibility to measure distance between the two centroids ?
> 
> It is also possible to define somehow centroid which will be automatically updated when position of the atoms (which are represented by this centroid) are changed - e.g. for different frames from the Amber MD trajectory ?
> 
>   Thank you in advance for your comments,
>      Best wishes,
> 
>           Marek
>