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

[Tom Goddard]

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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>>>
>