[Chimera-users] thermal ellipsoids

Eric Pettersen pett at cgl.ucsf.edu
Tue Jul 7 11:21:11 PDT 2009

On Jul 7, 2009, at 10:09 AM, Dipl.-Ing. Thomas Mitterfellner wrote:

> Hello again!
>> Currently it works only using the information in ANISOU records of  
>> PDB
>> files. You would just open the PDB file as usual, then use the  
>> Thermal
>> Ellipsoids tool (under Tools... Structure Analysis). It is fairly
>> self-explanatory, but there is also documentation -- just click the  
>> Help
>> button on the dialog or see the copy at our site:
>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/thermal/thermal.html 
>> >
> I'm very happy to see this working!
> At the risk of sounding ungrateful -- I'd like to request two  
> features.
> The first one: it is quite common to plot thermal ellipsoids on some
> probability level (e.g. 30% or 50%). Unfortunately, I don't know how
> these Values correspond to the scaling factor that currently controls
> the size of the ellipsoids. Could you implement this kind of scaling  
> as
> a feature or point out, if/how  these two measures correspond to  
> each other?

We intend to implement a probability-to-scaling-factor calculator in  
the interface, but haven't gotten there yet.  We felt that the tool  
was useful enough as is to put it out in what we consider to be an  
incomplete state.  As a stopgap for you, the scaling factor for 30% is  
1.1932 and for 50% is 1.5382.

> The second one: could you possibly implement it as a feature, that the
> lines resulting from the intersection of the main planes (xy, xz, yz)
> with the surface of the ellipsoid (the principal ellipses) can be
> displayed ?

Given the way the underlying ellipsoid depiction is generated, it  
won't be easy.  Nonetheless, I do think it should happen but it will  
take awhile.  One thing that would be easy for me to do would be to  
actually show the ellipsoid axes (as lines).  Would this help any if I  
put it in there?


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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