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

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu