[3dem] 3dem Digest, Vol 103, Issue 32

[Steve Chou]

Dear all,

Maybe my first email was not explicit enough. Here are more detailed
explanations.

In (both ideal and real) layer line images, the rise line is very special
--- it crosses meridian, but usually isn't visible due to low resolution.

Suppose there are two IDEAL helices whose building blocks (units) are very
similar, so the heights (Z) of the rise lines on these two layer line
images should be very similar (1/rise).

In the ideal helix with 13 (1300) units per 3 (300) turns, it can be
described as l=1300m+300n or l=13m+3n (this might annoy some people, but
it's just an ideal helix, imagined, not real, so it's fine). There should
be 1299 lines between equator and the rise line based on the first
equation, i.e., the rise line shows up at the 1300th line. These 1300 lines
are not all visible; actually, they merge into exact 13 lines (based on the
second equation).

In the other ideal helix with 1299 units per 300 turns, it can be described
as l=1299m+300n. There should be 1298 lines between equator and the rise
line, i.e., the rise line shows up at the 1299th line. In reality, these
1299 lines are not all visible; they also overlap/merge into 13 dominant
lines.

The 13th layer line (rise line) in the 1st ideal helix, now becomes 1299th
layer line in the 2nd ideal helix!!! The problem with the selection rule is
how to assign those 1299 layer line numbers. It's even impossible, so the
selection rule only applies to IMAGINED helices. This is the reason why
some people don't like the selection rule. If you use Z instead of l, you
won't be bothered with this (layer line number assignment/change).

In real world, if you just want to get an approximation of the helical
parameters using the selection rule, you can just treat 2nd helix the same
as the 1st helix. Therefore, you can still use the "selection rule". My
understanding is that it's just an ideal equation.

HTH,
Steve

On Thu, Mar 31, 2016 at 12:45 AM, <3dem-request at ncmir.ucsd.edu> wrote:

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>    1. Re: IHRSR++ and SPIDER 21.02 (Edward Egelman) (Hernando J Sosa)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 31 Mar 2016 04:44:47 +0000
> From: Hernando J Sosa <hernando.sosa at einstein.yu.edu>
> To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: Re: [3dem] IHRSR++ and SPIDER 21.02 (Edward Egelman)
> Message-ID:
>         <
> F0E461AAE34D0448B6EE7D31E433B708011AEEEAF5 at AEWEXCPM21.yuad.uds.yu.edu>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> As I see it both are equivalent descriptions of a helix. Given the rise
> and turn per subunit a selection rule can be generated and vice versa. An
> approximate selection rule (expressed as number of subunits and turns per
> repeat) can also be generated and from these values the rise and turn per
> subunit can also be calculated back.
> If you don't know the helical symmetry or your specimen testing tentative
> selection rules is very useful as they allow to quickly estimate their
> power spectrums (Bessel orders and layer line positions)  and compare them
> with the experimental data to find the best match (this could be
> complicated depending o the quality of the experimental power spectrums and
> possible  multiple near matches). Once you have a matching selection rule
> you automatically also have a pretty good estimate of the rise and turn per
> subunit of your helical specimen (but no handedness).  Once  good estimates
> of the rise and turn per subunit  are available  you could then forget
> about selection rules and use iterative refinement methods such as Ed's
> IRSHR to refine the structure.
> Best
> Hernando
>
> ________________________________
> From: 3dem [3dem-bounces at ncmir.ucsd.edu] on behalf of Steve Chou [
> stevezchou at gmail.com]
> Sent: Wednesday, March 30, 2016 9:03 PM
> To: 3dem at ncmir.ucsd.edu
> Subject: Re: [3dem] 3dem Digest, Vol 103, Issue 29
>
> 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<mailto:
> 3dem-request at ncmir.ucsd.edu>> wrote:
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> Today's Topics:
>
>    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<mailto:egelman at virginia.edu>>
> To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
> Cc: "Smith, Phillip R." <smithp01 at nyumc.org<mailto:smithp01 at nyumc.org>>
> Subject: Re: [3dem] IHRSR++ and SPIDER 21.02
> Message-ID: <56FBEDC7.7030904 at virginia.edu<mailto:
> 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>
> > <mailto: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
> <mailto: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<tel:434-924-8210>
> >>
> >> fax: 434-924-5069<tel:434-924-5069>
> >>
> >> egelman at virginia.edu<mailto:egelman at virginia.edu>
> >>
> >> http://www.people.virginia.edu/~ehe2n
> >>
> >> _______________________________________________
> >> 3dem mailing list
> >> 3dem at ncmir.ucsd.edu<mailto: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> <mailto:bullitt at bu.edu
> <mailto:bullitt at bu.edu>>
> > Telephone:  617-638-5037<tel:617-638-5037>
> > Facsimile:  617-638-4041<tel:617-638-4041>
> > http://www.bumc.bu.edu/phys-biophys/faculty/bullitt
> >
> >
> >
> > _______________________________________________
> > 3dem mailing list
> > 3dem at ncmir.ucsd.edu<mailto: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<tel:434-924-8210>
>
> fax: 434-924-5069<tel:434-924-5069>
>
> egelman at virginia.edu<mailto: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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-- 
Steven Chou
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