[EMAN2]On e2initialmodel parameter symmetry

[C.J.]

Dear all,

If I my object to be reconstrcuted is rod-liked or helix-liked, which
parameter of symmetry should I choose?

And I read the page(http://blake.bcm.tmc.edu/emanwiki/EMAN2/Programs/e2initialmodel),
and want to know what symmetry d<n> and h<n> stand for.

--
Regards!
C.J.

[Ludtke Steven]

Hi CJ. That depends on a lot of things. Certainly if you have a very long object (like a filament),
then it's likely (but not guaranteed, as some objects like amyloids can be irregular) to have helical
symmetry. However, if it's a short object, small enough to treat as a single particle, then the question
becomes whether you want to just reconstruct the helical domain that may exist in the central portion,
and ignore the ends, or reconstruct the whole thing. If you want to do the whole thing, then you
have to ask whether the objects are truly identical, or merely very similar. To do a single particle
reconstruction, the objects being reconstructed must be identical. If they aren't any aspects that
aren't identical will blur the structure. If the object is discretely heterogeneous. for example,
an object that is exactly 30,35,40 or 45 nm long depending on how many components it has, there
are methods for splitting the data into multiple homogeneous groups for reconstruction automatically
(multi-model refinement). If you have continuous heterogeneity (something flexible) or discrete
heterogeneity with a very large number of states, things will be very difficult.

EMAN2 does not yet have full support for doing true helical reconstructions. Nowadays these are
generally done with a method called IHRSR developed by Ed Egelman. EMAN2 has the beginnings of
support for this method, but it is likely to be another 6-12 months before we finish other
projects, and can get IHRSR finished. SPARX (ships with EMAN2) I believe does have an implementation,
but I don't know it's current status, you'd have to ask Pawel Penczek. Most people doing this
still use Ed's original IHRSR code which works in conjunction with Spider.

If it is an object you wish to treat as an isolated single particle (see the caveats above), then
you can use EMAN2 for it. The supported symmetries are described in the Wiki:
http://blake.bcm.edu/emanwiki/EMAN2/Symmetry

If you look at the power spectrum (Fourier transform) of an individual particle, do you observe layer lines ?
(it may be too small for them to be easily observed this way). Are the particles in different
orientations, or are they all lying flat on the grid ? How about the power spectrum of the class-averages,
assuming you made some ?

There's a lot involved in processing this type of object...

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[Arne]

Hi Steve,

I think this is related to the previous post:

I am trying to impose helical symmetry on a volume using the e2proc3d command and I can't get it to work.
More specifically I do not how to incorporate all the additional parameters (daz, tz and so on).
I am not sure where I am doing it wrong.
Could you post an exemplar e2proc3d command for helical symmetry?


Thank you very much,

Arne

[Paul Penczek]

Hi,

I do not know about e2proc3d, but the function is:

volh = vol.helicise(pixel_size,dp, dphi, fract, rmax, rmin)

fract =<1.0  is the fraction of z length of the volume used to helicise.

pixel_size and dp are in angstroms, rmax and rain in pixels.

Pawel Penczek.

---

From: Arne <derarne...@gmail.com>
To: em...@googlegroups.com
Sent: Fri, November 4, 2011 5:33:15 PM
Subject: Re: [EMAN2]On e2initialmodel parameter symmetry

[Steven Ludtke]

Just to help people get around the docs a bit more. From the wiki:

http://blake.bcm.edu/emanwiki/EMAN2/Symmetry

IHRSR is still something EMAN2 does incompletely, so documentation is not complete, anyway, the wiki says :

h - helical (not yet documented below, e2help.py symmetry -v 2 for more info)

 

---------------

e2help.py symmetry -v 2

...

h : Helical symmetry, with support for N-start, pitch and limited tilt range. Specify as H<nsym>,<nstart>,<daz>,<tz in pix>[,<maxtilt>]

apix(FLOAT) - Angstroms per pixel, default is 1.0, used only for tz

daz(FLOAT) - The rotational angle (about z) between successive identical subunits in degrees

maxtilt(FLOAT) - When generating projections, normally only 'side views' are created (3-D Z along Y in 2-D). This is the maximum out of plane tilt in degrees.

nstart(INT) - The Cn symmetry of a single Z-slice of the helix.

nsym(INT) - The number of asymmetric units to generate. This could be infinite for helical symmetry. Normally a multiple of nstart.

tz(FLOAT) - The translational distance (along z) between successive identical subunits in angstroms (default A/pix is 1)

...

-----------------

Following that information:

e2proc3d.py model_in.hdf model_out.hdf --sym=H50,3,4,10

would correspond to

nsym=50 copies

nstart=3

daz=4 degrees

tz=10 pixels

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Associate Professor, Dept. of Biochemistry and Mol. Biol.      Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel