[Chimera-users] Defining planes & Thermal ellipsoids

David Chenoweth dcheno at MIT.EDU
Mon Feb 22 12:20:32 PST 2010

Hi Elaine,

Thanks for the help! Everything works fine now, I just forgot to hit  
enter after entering the probability. I was also wondering if the ring  
fill color and transparency be changed independent of the rest of the  

Thanks again,

On Feb 20, 2010, at 1:26 PM, Elaine Meng wrote:

> Hi Dave,
> If you just want to fill rings, use the "fillring" command:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fillring.html>
> or you can create arbitrary polygons with BILD format:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html>
> The reason to use planes from Axes/Planes/Centroids is that they are  
> "smart" objects that can be used in distance and angle measurements  
> with atoms, axes, and centroids, as alluded to in my other replies  
> today.  If display is all you are concerned with, either of these  
> other methods will suffice.
> In Thermal Ellipsoids, the probability is working fine for me.  You  
> enter a number in the probability area and press return, which will  
> accordingly adjust the number shown in the "Scale factor" field.   
> Then that scale factor will be used the next time you click "Show  
> Ellipsoids" or choose one of the Thermal Ellipsoid presets.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/thermal/thermal.html 
> >
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                     http://www.cgl.ucsf.edu/home/meng/index.html
> On Feb 20, 2010, at 7:07 AM, David Chenoweth wrote:
>> Hi!
>> Thanks so much for adding the define plane and define centroid  
>> features. Is there any way to add the option of defining the border  
>> of the plane as a polygon where the selected atoms define the  
>> polygon vertices? This would allow a plane in the shape of a  
>> hexagon or any other heterocycle to be inset inside of an aromatic  
>> ring for example without the edges of the plane being visible  
>> outside the bond enclosed area.  Also, the thermal ellipsoid  
>> feature looks fantastic, however the probability setting doesn't  
>> seem to be functioning.
>> Thanks again for adding all these features,
>> Dave

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