[Chimera-users] centroids mutual distance etc. ?
marek.maly at ujep.cz
Sat Nov 29 06:18:30 PST 2014
thank you very much for the complex answer.
Dne Fri, 28 Nov 2014 19:22:53 +0100 Elaine Meng <meng at cgl.ucsf.edu>
> Hi Marek,
> If you made the centroids with “Axes/Planes/Centroids” (in menu under
> Tools… Structure Analysis) or command “define centroid”
> ...you can specify them by ID in the distance command, e.g.:
> distance c1 c1
> ...or measure distances using the GUI list of objects (for example,
> choosing two centroids in that list):
> 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
> …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 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:
>> 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,
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