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

Steven Ludtke sludtke at bcm.edu
Wed May 5 07:49:44 PDT 2010


I would tend to argue that Pawel and Joachim both have good points. If you are trying to compare with something like
the radius of gyration derived from solution scattering, the best approach would probably be to select a minimum reasonable
threshold and a maximum reasonable threshold (by eye) and establish a range of values consistent with your data. If you
treat the densities as a constant inside the isosurface as Joachim suggested, the linear transform you're applying to the densities
become meaningless. The radius of gyration is simply a function of shape.

However, if comparing with solution scattering is your aim (just a guess), you might consider just directly comparing the 1-D structure
factors from the two methods rather than a derived value like this.
----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Associate Professor
Co-Director National Center For Macromolecular Imaging
Dept of Biochemistry and Mol. Biol.
Baylor College of Medicine
sludtke at bcm.edu
stevel at alumni.caltech.edu
http://ncmi.bcm.edu/~stevel



On May 5, 2010, at 9:19 AM, Qiu-Xing Jiang wrote:

> 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)
>>> 
>>> 
>>> _______________________________________________
>>> 3dem mailing list
>>> 3dem at ncmir.ucsd.edu 
>>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem 
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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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