[Chimera-users] how to create a sphere in Chimera

[Ke Shyue-Chu]

Dear Elaine,
Your instruction works very well.
Thank you.
Sincerely,
Sc 

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Wednesday, March 11, 2020 9:32 AM
To: Ke Shyue-Chu <ke at gms.ndhu.edu.tw>
Cc: Chimera-users BB <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] how to create a sphere in Chimera

Hi Sc Ke,
Chimera doesn't do that projection calculation; you would have to do it yourself.  I think you could select all the nitrogens within the sphere and then write out their coordinates, but any other steps  after that would require your own processing.  You don't even need the sphere  (it may just be for display purposes) since you already have an atom at the center of it to define the radius for finding nitrogens.

I think you could select the nitrogens, for example, by just selecting the center atom (Ctrl-click on it, you may need to hide the sphere first if it's covering the atom), and then using a command something like:

select N & sel za<8.5

... where instead of 8.5 you would put the radius of the sphere.  It means select element N and also within 8.5 angstroms of current selection, which is the center atom you selected first.

You can hide the sphere by un-checking its S (Shown) checkbox in the Model Panel (show by choosing Model Panel from the Favorites menu).

Then you could get the coordinates of the selected nitrogens, for example with command

getcrd sel

... and then look in the Reply Log for the list of coordinates (show by choosing Reply Log from the Favorites menu).
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 10, 2020, at 6:05 PM, Ke Shyue-Chu <ke at gms.ndhu.edu.tw> wrote:
> 
> Hi, Elaine,
> Thank you for the detailed instruction. I got the sphere.
> 
> May I ask one more question:
> How do I define an equator plane of that sphere and project all nitrogen atoms within that sphere onto the equator plane; i.e. the polar coordinates of the nitrogen atoms within a sphere are what I would like to have?
> Thank you very much.
> sc
> 
> -----Original Message-----
> From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
> Sent: Thursday, March 05, 2020 12:46 AM
> To: Ke Shyue-Chu <ke at gms.ndhu.edu.tw>
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] how to create a sphere in Chimera
> 
> Hi Sc Ke,
> There is more than one way.  Say you have already selected the single 
> atom.  Then,
> 
> (A) to put a marker (essentially a fake atom) at that position, command “measure center”, for example:
> 
> measure center sel mark true radius 4.0 color pink model #8 
> transparency 50 #8
> 
> see manual for command options
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#c
> enter> 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.h
> tml>
> 
> (B) to put a spherical surface model at that position, command “shape sphere”, for example:
> 
> shape sphere radius 8.5 center sel color orange modelid #8 
> transparency 60 #8
> 
> see command options
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#sph
> ere>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry University of California, San 
> Francisco
> 
>> On Mar 4, 2020, at 2:40 AM, Ke Shyue-Chu <ke at gms.ndhu.edu.tw> wrote:
>> 
>> Hi,
>> I would like to know how to create a sphere of certain radius around a selected atom, for visualization purpose.
>> Thank you.
>> Sc Ke
>> Professor
>> Department of Physics
>> National Dong Hua University
>> Hualien, Taiwan
> 
> 
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