[3dem] determine spherically averaged radial density
Dieter Blaas
dieter.blaas at meduniwien.ac.at
Tue Apr 9 22:11:14 PDT 2024
Dear all,
thank you very much for your suggestions! We finally made it with
Eman2. I have just two last questions: 1) The curves are extremely noisy
- probably because of the high resolution and sharpening. Is it
legitimate to remove the very central density data and to filter the
volumes to lower resolution and/or to smoothen the curves (e.g. Bezier).
2) Is it correct that the final diameter corresponds to the value where
the curve passes zero density?
Thanks, best, Dieter
------------------------------------------------------------------------
Dieter Blaas,
Max Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
Tel: 0043 1 4277 61630,
Mobile: 0043 699 1942 1659
e-mail:dieter.blaas at meduniwien.ac.at
------------------------------------------------------------------------
On 09.04.2024 19:38, David Michael Belnap wrote:
>
> Another option is bradial in the Bsoft package (website, bsoft.ws).
> Here is an example command:
>
> bradial -verbose 7 -subtractbackground -radial -origin 142,142,142
> -minmax 0,150 -step 0.5 run_class001.mrc
>
> David
>
> =======================================
> David M. Belnap
> Electron Microscopy Core Laboratory
> Department of Biochemistry
> School of Biological Sciences
> 2501 SMBB
> University of Utah
> Salt Lake City, Utah 84112 USA
> Phone 801.585.1242
> FAX 801.587.3077
> David.Belnap at utah.edu <mailto:David.Belnap at utah.edu>
> =======================================
>
> *From: *3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Carlos Oscar
> Sorzano <coss at cnb.csic.es>
> *Date: *Tuesday, April 9, 2024 at 07:39
> *To: *Dieter Blaas <dieter.blaas at meduniwien.ac.at>, "Ludtke, Steven
> J." <sludtke at bcm.edu>, Tom Calcraft <tom.calcraft at crick.ac.uk>
> *Cc: *"3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> *Subject: *Re: [3dem] determine spherically averaged radial density
>
> Same here, I am afraid you would need to update the Xmipp if you still
> want to use it.
>
> Kind regards, Carlos Oscar
>
> El 09/04/2024 a las 14:39, Dieter Blaas escribió:
>
> Dear Tom and Steven,
>
> thanks for the quick answer! But I also need to install the
> entire Eman2 package for it work?
>
> Best, Dieter
>
> ------------------------------------------------------------------------
>
> Dieter Blaas,
>
> Max Perutz Laboratories
>
> Medical University of Vienna,
>
> Inst. Med. Biochem., Vienna Biocenter (VBC),
>
> Dr. Bohr Gasse 9/3,
>
> A-1030 Vienna, Austria,
>
> Tel: 0043 1 4277 61630,
>
> Mobile: 0043 699 1942 1659
>
> e-mail:dieter.blaas at meduniwien.ac.at
>
> ------------------------------------------------------------------------
>
> On 09.04.2024 13:47, Ludtke, Steven J. wrote:
>
> To add, if your goal is to compute the radial density
> distribution as a curve rather than the averaged volume,
>
> e2proc3d.py --calcradial 0 map.mrc radial.txt
>
> (can also calculate min,max)
>
> e2proc3d.py --help
>
> ---
>
> Steven Ludtke, Ph.D. <sludtke at bcm.edu>
> <mailto:sludtke at bcm.edu> Baylor College
> of Medicine
> Charles C. Bell Jr., Professor of
> Structural Biology Dept. of Biochemistry
> Deputy Director, Advanced
> Technology Cores and Molecular Pharmacology
> Academic Director, CryoEM Core
> Co-Director CIBR Center
>
>
>
> On Apr 9, 2024, at 5:34 AM, Tom Calcraft
> <tom.calcraft at crick.ac.uk>
> <mailto:tom.calcraft at crick.ac.uk> wrote:
>
> Hi Dieter,
>
> The math.rotationalaverage function in EMAN2’s e2proc3d.py
> should do what you are looking for:
>
> e2proc3d.py --process=math.rotationalaverage input.mrc
> output.mrc
>
> Best,
> Tom
>
>
> On 9 Apr 2024, at 10:33, Dieter Blaas
> <dieter.blaas at meduniwien.ac.at> wrote:
>
>
> External Sender: Use caution.
>
>
> Dear all,
>
> we need to determine the spherically averaged radial
> density of a
> symmetric virus. Long ago, we used for this
> xmipp_operate but my old
> scipion3 and xmipp installs do not work any more. Is
> there any other
> piece of software that can easily do this without too
> much ado?
>
> Thanks for hints, Dieter
>
> ------------------------------------------------------------------------
> Dieter Blaas,
> Max Perutz Laboratories
> Medical University of Vienna,
> Inst. Med. Biochem., Vienna Biocenter (VBC),
> Dr. Bohr Gasse 9/3,
> A-1030 Vienna, Austria,
> Tel: 0043 1 4277 61630,
> Mobile: 0043 699 1942 1659
> e-mail: dieter.blaas at meduniwien.ac.at
> ------------------------------------------------------------------------
>
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