[3dem] RE: Radius of Gyration from a single particle 3-D model

[Qiu-Xing Jiang]

For CG 3, here what I do. 1) find a proper threshold to account for molecule size, 2) generate a mask around the molecule, and calculate the s.d. of the volxels outside the mask; 3) divide the map by the s.d. of the noise, and subtract one from the map; 4)  find the right threshold and use it in CG 3. It generates a weight function. For symmetrical densities, the voxels around the symmetry axis tend to be over-weighted in this procedure, and the radius could be smaller. From run to run in refinement, the results change a bit, but not much when the refinement converges well. 


>>> Joachim Frank <jf2192 at columbia.edu> 5/4/2010 11:57 PM >>>
However, when a choice of surface threshold has already been made,  
which is often the case, then I suggest you can replace the inside  
with 1's and the outside with 0's, so CG 3 will give you the rad of  
gyration and center of gravity for a mass of that shape.

--Joachim.

Pawel.A.Penczek at uth.tmc.edu
Quoting "Penczek, Pawel A" <>:

> Hi,
>
> indeed, I wrote CG 3 while back.  However, strictly speaking neither  
>  radius of gyration
> nor center of gravity can be computed for EM reconstructed molecules  
>  as proper
> normalization of densities is not known.  So, it is easy to check   
> that results are arbitrary and
> can be modified significantly by renormalization of the structure.
>
> Regards,
> Pawel A. Penczek, Ph.D.
> Professor
> Department of Biochemistry and Molecular Biology
> The University of Texas - Houston Medical School
> MSB 6.220
> 6431 Fannin
> Houston, TX 77030
> USA
>
> phone: 713-500-5416
> fax: 713-500-6297
> pawel.a.penczek at uth.tmc.edu 
> http://www.uth.tmc.edu/bmb/faculty/pawel-penczek.html 
> ________________________________________
> From: 3dem-bounces at ncmir.ucsd.edu [3dem-bounces at ncmir.ucsd.edu] On   
> Behalf Of Wang, Hongwei [hongwei.wang at yale.edu] 
> Sent: Tuesday, May 04, 2010 9:22 PM
> To: 3dem at ucsd.edu 
> Subject: [3dem] RE: Radius of Gyration from a single particle 3-D model
>
> For those who have the same question as I, this is an answer from Qiu-Xing:
> spider has a program, cg 3
>
>> -----Original Message-----
>> From: 3dem-bounces at ncmir.ucsd.edu [mailto:3dem-bounces at ncmir.ucsd.edu] On
>> Behalf Of Wang, Hongwei
>> Sent: Tuesday, May 04, 2010 12:02 AM
>> To: 3dem at ucsd.edu 
>> Subject: [3dem] Radius of Gyration from a single particle 3-D model
>>
>> Dear Colleagues,
>>
>> I am wondering if there's a quick way to calculate the radius of gyration
>> from the 3-D model of a single particle reconstruction.
>>
>> Thanks for your reply.
>>
>> Hongwei
>>
>> -------------------------------------
>> Hongwei Wang, Ph.D.
>> Assistant Professor
>> Dept. Molecular Biophysics & Biochemistry
>> Yale University School of Medicine
>> 333 Cedar Street
>> P.O. Box 208024
>> New Haven, CT 06520-8024
>> 203-785-3322 (O)
>>
>>
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>



-- 
Joachim Frank, Ph.D.
Howard Hughes Medical Institute Investigator,
Professor, Department of Biochemistry and Molecular Biophysics,
and Department of Biology, Columbia University,
650 West 168th Street, P&S Black 2-221
New York, NY 10032
(T) 212 305-9510  (F) 212 305-9500  Admin Asst: Tornubari Barinee 212 305-9512
(E) jf2192 at columbia.edu 
http://www.hhmi.org/research/investigators/frank.html 
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