[3dem] 3dem Digest, Vol 103, Issue 29
Steve Chou
stevezchou at gmail.com
Wed Mar 30 18:03:48 PDT 2016
Dear all,
My understanding on this topic (could be completely wrong) is described
here:
Suppose there are two "ideal helices": one is 1299 units per 300 turns;
the other 13 (1300) units per 3 (300) turns. To describe them using the
selection rule, they are l=1299m+300n, and l=13m+3n, respectively.
The power spectra (layer line images) of these two ideal helices will be
SIMILAR in biological EM conditions [biological molecular building blocks
(units) in the EM RESOLUTION RANGE] --- Biology (filaments length,
flexibility, etc. usu. the main reason) introduces ambiguity here. The
layer line image of the helix with 1299 units per 300 turns should have
more layer lines in a specific height than the other one, but usually not
noticeable in biological EM conditions. Bessel orders (n) for each layer
line on these two layer line images are the same, and the heights (Z) of
dominant/obvious layer lines change a little bit --- may not be noticeable
either, however, the LAYER LINE NUMBERS (l) will be TOTALLY DIFFERENT. I
think this is the reason why some people don't like this (layer line number
change). If you don't want be be bothered by the layer number change during
the interpretation of the layer line image, then Ed's point is absolutely
correct [to use Z instead of l (implying that you are using selection
rule)].
In real world, it should be fine to describe a helix with 1299 units per
300 turns as 13 (1300) units per 3 (300) turns. This is because the
helicity of a helix data set is a range (e.g., between 1297 units per 300
turns and 1301 units per 300 turns).
In biological X-ray crystallography, the assemblies of the molecules in the
crystals are not perfect either, but crystallographers just force them to
be in a specific space group, usually choose the highest reasonable
symmetry.
Another point: As Ed said, I don't think Fourier-Bessel reconstruction
actually needs (relies on) the selection rule.
Idealists can think filaments using the selection rule (units and turns)
and symmetry (non-helical); realists may like to describe them using only
rise and rotation, plus symmetry --- this is more practical. Both are fine,
especially for easy cases. For complicated cases, it might take a LONG time
(months) to figure out the helical parameters.
All the best,
Steve
On Wed, Mar 30, 2016 at 11:16 AM, <3dem-request at ncmir.ucsd.edu> wrote:
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> 1. Re: IHRSR++ and SPIDER 21.02 (Edward Egelman)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 30 Mar 2016 11:16:23 -0400
> From: Edward Egelman <egelman at virginia.edu>
> To: 3dem at ncmir.ucsd.edu
> Cc: "Smith, Phillip R." <smithp01 at nyumc.org>
> Subject: Re: [3dem] IHRSR++ and SPIDER 21.02
> Message-ID: <56FBEDC7.7030904 at virginia.edu>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> This is an incredibly belated reply. I never responded at the time since
> I did not want to beat a living horse (I had assumed that the horse was
> dead, but I was quite wrong). But a discussion I had yesterday made me
> realize that a response might be useful. Esther has raised that knowing
> that a structure can vary from 13 subunits in 6 turns to 11 subunits in
> 5 turns provides a helpful description of the variability. This is only
> a change in twist, which is from 166.15 degrees per subunit (13/6) to
> 163.64 degrees per subunit (11/5). But how useful is it describing the
> variability in twist in terms of a repeat either every 5 or 6 turns? A
> structure with 24 subunits in 11 turns would be between these two, and
> have 165.0 degrees rotation per subunit. A structure with 46 subunits in
> 21 turns would have 164.35 degrees, also between 13/6 and 11/5. As would
> 174/80, 186/85, 291/134, etc. If it is obvious to anyone that all of
> these ratios fall within Esther's range, then I am the one who is
> challenged. Simply stating at the outset that the twist ranges from
> 163.64 to 166.15 degrees is much easier, more intuitive and much more
> helpful (in my opinion).
> Regards,
> Ed
>
> On 3/6/16 8:25 AM, Bullitt Esther wrote:
> > Are we really going to get into this?
> >
> > I am in general a reasonable person, and I still find selection rules
> > to be a good way to get an intuitive feeling for the structure of a
> > helical filament.
> >
> > Is it the be-all, end-all? Of course not.
> > Is it a useful approximation as a start for understanding the biology?
> > Yes, it is.
> > For example, if one determines that filaments you analyze range from
> > 13 u/ 6 t to 11u / 5 t, that gives a visual meaning to how much
> > the filament tightens/loosens while performing its functions.
> > Necessary for structure determination? Not really. Helpful? In my
> > opinion, yes.
> >
> > In addition to the references Ed suggested, I am a fan of Murray
> > Stewart's 1988 article, 'Computer Image Processing of Electron
> > Micrographs of Biological Structures with Helical Symmetry' , in J
> > Electron Microscopy Technique 9:325-358
> >
> > Sincerely,
> > Esther
> >
> > On Mar 5, 2016, at 10:36 AM, Edward Egelman <egelman at virginia.edu
> > <mailto:egelman at virginia.edu>> wrote:
> >
> >> No reasonable person would use selection rules any more. They were
> >> formulated in the 1950s and arise from a crystallographic-type
> >> formulation where a helix is described by the ratio of integers
> >> (units/turn or u/t). For real helices, the best description is given
> >> by two real numbers, a rise (Angstroms) and a rotation (degrees). The
> >> description of those tubes (I assume) is given in Parent et al.,
> >> Physical Biology:
> >>
> >> doi:10.1088/1478-3975/7/4/045004
> >>
> >> Regards,
> >> Ed
> >>
> >> On 3/5/16 9:49 AM, Smith, Phillip R. wrote:
> >>> The data and tutorial that you point to is indeed excellent and a nice
> testbed for software.
> >>>
> >>> But it would be a huge help if someone could provide the selection
> rule for the F170A tubes in the data provided, p8:
> >>>
> >>> "The values for the symmetry parameters ([Cn], [rise], [deltaphi])
> were derived from the diffraction pattern (derivation not shown).?
> >>>
> >>> Hope you can help?
> >>>
> >>> Very best to all!
> >>>
> >>> -Ross Smith-
> >>>
> >>>> On Feb 29, 2016, at 4:39 PM, Edward Egelman<egelman at virginia.edu>
> wrote:
> >>>>
> >>>> Hi,
> >>>> Unfortunately, there are no good tutorials. Also, the more that I
> learn the more I realize that it is not as simple as I originally assumed.
> I would suggest reading three papers as a start:
> >>>>
> >>>> Egelman, E.H. (2010), ?Reconstruction of Helical Filaments and
> Tubes?, Methods in Enzymology 482, 167-183.
> >>>>
> >>>> Egelman, E.H. (2014). ?Ambiguities in helical reconstruction?. eLife
> 3:e04969 doi:10.7554/eLife.04969.
> >>>>
> >>>> Egelman, E.H. (2015). ?Three-dimensional reconstruction of helical
> polymers?, Archives of Biochemistry and Biophysics 581, 54-58.
> >>>>
> >>>> Regards,
> >>>> Ed
> >>>>
> >>>>
> >>>> On 2/29/16 2:58 PM, Johannes Haataja wrote:
> >>>>> Dear all,
> >>>>> thank you for the replies. I now have an older version of spider.
> >>>>>
> >>>>> Regarding IHRSR Prof. Egelman - what would the recommended
> way/tutorial
> >>>>> for learning to use IHRSR?
> >>>>>
> >>>>> My best,
> >>>>> - J.
> >>>>>
> >>>>> P.S. I guess ideally one would just read an article about the theory
> and
> >>>>> unix/linux man-pages of relevant command line tools and then
> inductively
> >>>>> reason how one must proceed to apply the method to the problem at
> hand.
> >>>>> Since I lack such a tenacity, I usually look for tutorials in order
> to
> >>>>> understand how the softwares/black boxes work. Also, I imagine that
> for
> >>>>> helical reconstruction, like for any inverse problem, there are many
> >>>>> different methods for recovering the quantit(y/ies) of interest and
> that
> >>>>> people usually are hesitant to openly aside with particular approach
> may
> >>>>> it be the right one or obviously the wrong one (e.g. Bayesian vs.
> >>>>> Frequentist interpretation of statistics) ;).
> >>>>>
> >>>>>
> >>>>>
> >>>>> ma, 2016-02-29 kello 12:13 -0500, Michael Radermacher kirjoitti:
> >>>>>
> >>>>>> I would contact the people in Albany and also
> >>>>>> discuss with them the problem you are having
> >>>>>> with your version.
> >>>>>>
> >>>>>> Michael
> >>>>>>
> >>>>>> On 2/29/2016 11:46 AM, Johannes Haataja wrote:
> >>>>>>
> >>>>>>> Hi,
> >>>>>>> does anyone know where to obtain old versions of SPIDER,
> namely v.
> >>>>>>> 21.02? The oldest from download page is 21.11. The reason for
> asking is
> >>>>>>> that I need and older SPIDER version to test IHRSR++ v. 1.5
> tutorial
> >>>>>>>
> >>>>>>>
> >>>>>>> http://cryoem.ucsd.edu/wikis/software/start.php?id=ihrsr
> >>>>>>>
> >>>>>>>
> >>>>>>> to exclude the possibility that the errors I run into (in the final
> >>>>>>> reconstruction step) have something to do with SPIDER version.
> >>>>>>>
> >>>>>>> My best,
> >>>>>>> - J.
> >>> ------------------------------------------------------------
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> >>> =================================
> >>
> >> --
> >>
> >>
> >>
> >> Edward H. Egelman, Ph.D.
> >>
> >> Harrison Distinguished Professor
> >>
> >> Dept. of Biochemistry and Molecular Genetics
> >>
> >> University of Virginia
> >>
> >> phone: 434-924-8210
> >>
> >> fax: 434-924-5069
> >>
> >> egelman at virginia.edu
> >>
> >> http://www.people.virginia.edu/~ehe2n
> >>
> >> _______________________________________________
> >> 3dem mailing list
> >> 3dem at ncmir.ucsd.edu <http://ncmir.ucsd.edu>
> >> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
> >
> > ---
> > Esther Bullitt, Ph.D.
> > Dept. of Physiology & Biophysics
> > Boston University School of Medicine
> > 700 Albany Street, Room W302
> > Boston, MA 02118-2526
> >
> > Email: bullitt at bu.edu <mailto:bullitt at bu.edu>
> > Telephone: 617-638-5037
> > Facsimile: 617-638-4041
> > http://www.bumc.bu.edu/phys-biophys/faculty/bullitt
> >
> >
> >
> > _______________________________________________
> > 3dem mailing list
> > 3dem at ncmir.ucsd.edu
> > https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>
> --
>
>
>
> Edward H. Egelman, Ph.D.
>
> Harrison Distinguished Professor
>
> Dept. of Biochemistry and Molecular Genetics
>
> University of Virginia
>
> phone: 434-924-8210
>
> fax: 434-924-5069
>
> egelman at virginia.edu
>
> http://www.people.virginia.edu/~ehe2n
> <http://www.people.virginia.edu/%7Eehe2n>
>
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--
Steve Chou
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