[Chimera-users] (Thermal ellipsoids) anisotropic temperature factor ellipsoids

Tom Goddard goddard at cgl.ucsf.edu
Fri Dec 12 10:27:03 PST 2008

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)


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


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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