Hi David, Ok I see now, it's a matter of choosing the size of each ellipsoid to have a 50% chance of finding the atom in that volume. This shouldn't be too hard but I'll let Eric tackle it if he has time. Tom David Chenoweth wrote:

Hi Tom,

Here is the description of the thermal ellipsoids and option to change the probability lavel from the Raster3D page.

-prob Plevel By default, isosurfaces are drawn to enclose the 50% probability level in the probability density function described by the Uij values in the ANISOU record. The -prob option allows you to select a different probability level instead. If 0<Plevel<1 this value is interpreted as a fraction; if Plevel > 1 this value is interpreted as a percent.

http://skuld.bmsc.washington.edu/raster3d/html/rastep.html

-Dave

On Dec 12, 2008, at 10:27 AM, Tom Goddard wrote:

...

Hi David,

By probability level do you mean occupancy? You could change the script to show only atoms with > 50% occupancy by changing:

for a in atoms: perMol.setdefault(a.molecule, []).append(a)

to

for a in atoms: if a.occupancy > 0.5: perMol.setdefault(a.molecule, []).append(a)

Tom

David Chenoweth wrote:

...

Hi Tom,

Thanks for the script and all the help. The script works great, but I was just wondering if there is a way to set a probability level (50%)?

Thanks again, Dave

On Dec 12, 2008, at 9:58 AM, Tom Goddard wrote:

...

The script for drawing aniosotropic b-factor ellipsoids makes uses 1280 triangles per ellipsoid surface which slows down your graphics for cases with more than 1000 ellipsoids. You can reduce the "subdivision_levels = 3" in the script to "subdivision_levels = 1" to use just 80 triangles, or to a value of 2 for 320 triangles. The number of triangles controls how smooth the ellipsoid looks (T = 20 * 4^S, S = subdivision_levels).

Tom

Eric Pettersen wrote:

...

On Dec 10, 2008, at 3:41 PM, David Chenoweth wrote:

...

Dear Chimera team,

It looks like preserving PDB ANISOU in Chimera is now a solved problem and I was just wondering if the ability to display anisotropic temperature factor ellipsoids would be added soon. Our small molecule lab and molecular observatory at Caltech is starting to use Chimera and I think small molecule crystallography labs in general would use Chimera more if this feature were available. I do have to admit that I am interested in this feature for selfish reasons. I am using Chimera for several publications and for the graphics in my thesis which, has to be finished in the next couple of weeks, and I would really like to use this feature.

Hi Dave, Yes, reading/preserving the ANISOU info lays the groundwork for eventually showing anisotropic ellipsoids. There's still a lot of work to go before showing the ellipsoids becomes a usable feature of Chimera. It might make it into our next release (middle of next year) and it might not. As a stopgap, I've attached a script that will show ellipsoids for any currently selected atoms. You can run it by simply using File->Open or the "open" command. The first two lines of the script control the size and color of the ellipsoids, so change them if you like. The script leverages some code that Tom Goddard wrote for showing principal axes of inertia as an ellipsoid. Good luck with the thesis!

--Eric

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

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