[3dem] Any scripts to determine the rotation symmetry

Gomez, Yacob yacob.gomez at mssm.edu
Sat Oct 13 08:57:53 PDT 2012

In case you want to use Xmipp, follow the steps 10 to 14 of this Nature Protocols paper:
Scheres SH, Núñez-Ramírez R, Sorzano CO, Carazo JM, Marabini R., Nat Protoc. 2008;3(6):977-90
You would get a result like the figure 3, where you can select easily groups of particles according to their symmetry.

Assuming 64x64 images, centered and aligned, a simple script would be these 3 commands:
xmipp_make_spectra -i images.sel -o images.sim -x0 32 -y0 32 -r1 0 -r2 25
xmipp_classify_kerdensom -i images.sim -o kerd -xdim 7 -ydim 7 -reg0 1000 -reg1 200 -steps 5
xmipp_show -spectsom kerd -din images.sim

You should play with the parameters reg0, reg1, xdim and ydim. And also determine the radious r2 for your particles.

The input file "images.sel" is a "selection file": a text file with one line per file, followed by "1", that indicates the image is active. Each file should be a single image in Spider format.
Something like this:
my_images/image000357.spi 1
my_images/image000359.spi 1
my_images/image000371.spi 1
my_images/image000372.spi 1

It runs in a few hours in a single CPU.


From: 3dem-bounces at ncmir.ucsd.edu [3dem-bounces at ncmir.ucsd.edu] on behalf of Marin van Heel [m.vanheel at imperial.ac.uk]
Sent: Saturday, October 13, 2012 2:21 AM
To: Dai, Aguang
Cc: 3dem at ncmir.ucsd.edu
Subject: Re: [3dem] Any scripts to determine the rotation symmetry

Dear Aguang Dai,

The estabished way to analyse the symmetry properties of a data set is through eigenvector analysis  (see: P Dube, P Tavares, R Lurz, and M van Heel, Bacteriophage SPP1 portal protein: a DNA pump with 13-fold symmetry, EMBO J. 12 (1993) 1303-1309.) Further details in the Symmetry and MSA  manuals/papers on: http://www.single-particles.org/methodology.html.

Hope this helps,

Marin van Heel


On 12-Oct-12 8:28 PM, Dai, Aguang wrote:
Hello everyone,

I'm working on some macromolecules with symmetry.
Unfortunately, it shows combination of different symmetry.
I want to know the intrinsic symmetry inside.
I'm wondering anyone has or knows any script to determine the rotation symmetry in 3D volume.
Thanks a lot.

Best wishes,
Aguang Dai

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    Marin van Heel

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