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<div class="moz-cite-prefix">Hi Bala,<br>
<br>
I think the easiest way to show circles is to use the shape
command to show a cylinder, for example.<br>
<br>
shape cylinder radius 20 height 1 slab 1 color pink<br>
<br>
I guess you want to have it perpendicular to the screen and
centered on some atoms. That bit is slightly tricky. You can use
<br>
<br>
shape cylinder radius 20 height 1 slab 1 color pink center
#3:82-84@CA<br>
<br>
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@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.<br>
<br>
Tom<br>
<br>
<br>
<br>
<br>
-------- Original Message --------<br>
Subject: Re: [Chimera-users] drawing circles<br>
From: Elaine Meng<br>
To: Bala subramanian <br>
Date: 9/24/12 9:46 AM<br>
</div>
<blockquote
cite="mid:D44627F4-217B-47DD-996C-C136CE44803A@cgl.ucsf.edu"
type="cite">
<pre wrap="">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.
<a class="moz-txt-link-rfc2396E" href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#objectlist"><http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#objectlist></a>
(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:
<a class="moz-txt-link-rfc2396E" href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html"><http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html></a>
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:
<a class="moz-txt-link-rfc2396E" href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/symbols.html"><http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/symbols.html></a>
(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
</pre>
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<pre wrap="">
On Sep 24, 2012, at 9:17 AM, Bala subramanian wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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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