[Chimera-users] centroids mutual distance etc. ?

Marek Maly marek.maly at ujep.cz
Sat Nov 29 06:18:30 PST 2014


Dear Elaine,

thank you very much for the complex answer.

    Best wishes,

        Marek

Dne Fri, 28 Nov 2014 19:22:53 +0100 Elaine Meng <meng at cgl.ucsf.edu>  
napsal/-a:

> 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
>>
>
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