[3dem] determine spherically averaged radial density

Tue Apr 9 10:38:30 PDT 2024

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<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>
------------------------------------------------------------------------

_______________________________________________
3dem mailing list
3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwIGaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=YqSKINRR3R2v26j2eOLZWTPqJJe4nGNsH_2SW2O5zbAgeBL1B3L83CqZkS3m5Pi7&s=r0LHGODmqJ5vbDIVB-Ul7WI7CIICRXsT46di8CIMd7g&e=

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT
_______________________________________________
3dem mailing list
3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwIGaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=YqSKINRR3R2v26j2eOLZWTPqJJe4nGNsH_2SW2O5zbAgeBL1B3L83CqZkS3m5Pi7&s=r0LHGODmqJ5vbDIVB-Ul7WI7CIICRXsT46di8CIMd7g&e=

_______________________________________________

3dem mailing list

3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>

https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20240409/59865fee/attachment.html>