[Chimera-users] drawing circles

Tom Goddard goddard at sonic.net
Mon Sep 24 13:50:39 PDT 2012

Hi Bala,

   I think the easiest way to show circles is to use the shape command 
to show a cylinder, for example.

     shape cylinder radius 20 height 1 slab 1 color pink

I guess you want to have it perpendicular to the screen and centered on 
some atoms.  That bit is slightly tricky.  You can use

     shape cylinder radius 20 height 1 slab 1 color pink center #3:82-84 at CA

but the plane of the circle will be perpendicular to the z-axis of the 
molecule #3 coordinate system which won't be the same as the z-axis of 
the screen if you did any rotation.  A trick to handle this problem is 
open your molecule and don't rotate, make the circle, and set the center 
of rotation to the center of the circle (cofr #3:82-84 at CA), freeze the 
circle (Favorites / Model Panel, deactivate cylinder), then rotate the 
molecule to the orientation you want.  If you translate the molecule 
make sure to unfreeze the circle first.


-------- Original Message --------
Subject: Re: [Chimera-users] drawing circles
From: Elaine Meng
To: Bala subramanian
Date: 9/24/12 9:46 AM
> Hi Bala,
> You can change the color (including transparency) of planes, axes, centroids by clicking a color well in the table of such objects and using the Color Editor.  However, there is no separate fill, it is just the color of the whole object.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#objectlist>
> (In recent versions of Chimera you can also just select the plane with mouse Ctrl-click and use the menu, Actions... Color... from editor)
> Alternative ways to draw rings:
> (1) just add a 2D Label circle symbol, increase font size and color as desired.  You can have multiple labels of different font sizes and colors.  As the name suggests, 2D labels exist only in the 2D plane and do not move along with the 3D Chimera view... however, you can drag each to the desired X,Y location:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html>
> You can copy-and-paste into the label field, for example from this page of symbols.  The circle is the top symbol in the "Miscellaneous" column:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/symbols.html>
> (2) create a surface model shaped like a ring by opening the attached python script.  Inner/outer radii and color can be changed by editing the script.  This will exist in 3D, so if you want it to look like a circle be careful to only translate (not rotate) it.
> 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 Sep 24, 2012, at 9:17 AM, Bala subramanian wrote:
>> Friends,
>> I want to draw concentric circles of increasing sizes around the
>> protein. To achieve this, i used the 'define plane' option to draw
>> disk choosing I three reference atoms and drew the disks of increasing
>> sizes and choose two different color for the inner and outer disk.
>> Since the reference atoms are the same. If i change the color of the
>> bigger disk, i get a weird appearance of the inner disk. I dnt know
>> how to resolve this problem.
>> I would like to know if i can do something like making the disk
>> transparent/removing the fill color of the disk.
>> thanks,
>> Bala
>> -- 
>> C. Balasubramanian
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> Chimera-users at cgl.ucsf.edu
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