[3dem] determine spherically averaged radial density
Tom Calcraft
tom.calcraft at crick.ac.uk
Wed Apr 10 00:39:53 PDT 2024
That depends on what you are using the curve for. Filtering or downsampling (of either the map itself or the rotational average) are both good ways to tidy up the curve. Regarding the "final diameter”, it is up to your judgement where to draw the line - there may be non-zero background density on the inside/outside of your spherical virus even after rotational averaging. It is probably best to check your diameter value(s) against the high-resolution map without rotational averaging, or against an atomic model if you have one available.
Best,
Tom
On 10 Apr 2024, at 06:11, Dieter Blaas <dieter.blaas at meduniwien.ac.at> wrote:
External Sender: Use caution.
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<mailto: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><mailto:3dem-bounces at ncmir.ucsd.edu> on behalf of Carlos Oscar Sorzano <coss at cnb.csic.es><mailto:coss at cnb.csic.es>
Date: Tuesday, April 9, 2024 at 07:39
To: Dieter Blaas <dieter.blaas at meduniwien.ac.at><mailto:dieter.blaas at meduniwien.ac.at>, "Ludtke, Steven J." <sludtke at bcm.edu><mailto:sludtke at bcm.edu>, Tom Calcraft <tom.calcraft at crick.ac.uk><mailto:tom.calcraft at crick.ac.uk>
Cc: "3dem at ncmir.ucsd.edu"<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu><mailto: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<mailto: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<mailto: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<mailto:dieter.blaas at meduniwien.ac.at>
------------------------------------------------------------------------
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