EMAN2 Tomography Tutorial

[Aditya Behal]

Hi,

Is there a detailed EMAN2 tomography tutorial that can lead me through the GUI or command line?

http://blake.bcm.edu/emanwiki/EMAN2/Programs/e2tomoboxer 

I'm not sure if the above link contains outdated information (good only for EMAN2.12). I tried running some of those commands unsuccessfully.

Thanks for the help.

Aditya

[Steve Ludtke]

Yes, there are tutorials posted, look further down the page

http://blake.bcm.edu/emanwiki/e2tomo

http://blake.bcm.edu/emanwiki/EMAN2/Programs/tomoseg

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

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[Aditya Behal]

I'm trying to download the ribosomal data that the tomography tutorial is using. The tutor says to download the data from https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10064/. 

I check the box next to "data 33.9 GB" and click download. The Aspera option doesn't work for me (I'm using a mac FYI). The second option (uncompressed) lets me download 30 GB+ data. When it's finished downloading, I clicked on the data.zip to unzip it; however, archive utility says there is nothing to expand. However, I can't see the data. I just see one file called archive.zip

Any help is appreciated.

Thanks,

Aditya

[Steve Ludtke]

Hi Aditya,

this is really a question for the Empiar folks, not us. I too find Aspera annoying, but the Empiar developers really like it. Is the downloaded file the expected size?  Did you install and try Aspera?  You really need to speak to the Empiar developers.

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

Co-Director National Center For Macromolecular Imaging                  (ncmi.bcm.edu)

[Tanvir Shaikh]

On 15. Sep 2018, at 08:20, Aditya Behal <aditya....@gmail.com> wrote:

> I'm trying to download the ribosomal data that the tomography tutorial is using. The tutor says to download the data from https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10064/.
>
> I check the box next to "data 33.9 GB" and click download. The Aspera option doesn't work for me (I'm using a mac FYI). The second option (uncompressed) lets me download 30 GB+ data. When it's finished downloading, I clicked on the data.zip to unzip it; however, archive utility says there is nothing to expand. However, I can't see the data. I just see one file called archive.zip

FTP also works. The URL ftp://ftp.ebi.ac.uk/pub/databases/empiar/archive/10064/data/ contains the data.

There are graphical FTP clients, but I haven’t used them. I tested that anonymous FTP works from the command line for EMPIAR, using ‘ftp’ as the username.

Random trick:
curl -s ftp://ftp.ebi.ac.uk/pub/databases/empiar/archive/10064/data/
writes a list of files, and if you know some shell scripting, you can download/process the files one at a time. I did this for downloading micrograph movies from EMPIAR, running MotionCor on the fly rather than downloading terabytes of data.

I have notes on how to use Aspera on another computer, but I try to avoid it if possible.

-Tapu Shaikh

[Aditya Behal]

Thanks for the feedback. I also found that using the unzip command in terminal works as well. For some reason, archive utility doesn’t like expanding this file.

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From: 30071116000n behalf of
Sent: Monday, September 17, 2018 5:29 AM
To: em...@googlegroups.com
Subject: Re: [EMAN2] EMAN2 Tomography Tutorial

 

[Aditya Behal]

My Mac is crashing on the 3D reconstruction step. My Mac has an i7 processor, and the tutorial says running 6-8 threads should be ok with i7. I’ve tried 8 and then 6. I’ve even lowered the threads to 4, but my mac still crashes.

 

By “crashing,” I mean that the process takes forever (overnight, the process doesn’t finish while the tutorial says with 12 threads it should take 8-12 minutes). It gets so bad that I can’t even log onto my Mac (it doesn’t let me type my password) unless I force the system to restart and kill the program.

 

I’m using EMAN 2.21 right now.

 

Any ideas on what I can do?

 

Thanks,

 

Aditya

 

From: Steve Ludtke
Sent: Saturday, September 15, 2018 4:27 AM
To: em...@googlegroups.com

[Steve Ludtke]

Hi Aditya,

I fear we need more information to offer any useful advice. Which tutorial are you reading?  The most recent tutorial for subnanometer resolution subtomogram averaging uses software that didn't exist in the release version of EMAN2.21, so...

1) what is the full output of e2version.py on your computer?

2) which tutorial are you trying to follow?

3) which data set are you using? the one suggested in the tutorial?

4) what is the full command-line of the command you are running which is failing? (you can get this from the 'command' tab in the project manager or the .eman2log.txt file)

5) how much RAM does your computer have?

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

[Aditya Behal]

Hi Steve, 

1) Full output of e2version.py:

EMAN 2.21a final (GITHUB: 2018-08-03 17:12 - commit: 29ca8aafd )

Your EMAN2 is running on: Mac OS 10.13.6 x86_64

Your Python version is: 2.7.15

2) I was using the tutorial at http://blake.bcm.edu/emanwiki/e2tomo. There used to be a PDF of the tutorial on this website, but I can't find it anymore. I've attached the tutorial PDF that I'm referencing.

3) I'm using the ribosomal tutorial data set; I downloaded it from the link referenced in the tutorial PDF.

4) Command that I'm running that causes the computer to crash:

e2tomogram.py tiltseries/CTEM_tomo1.hdf tiltseries/CTEM_tomo2.hdf tiltseries/CTEM_tomo3.hdf tiltseries/VPP_tomo1.hdf tiltseries/VPP_tomo2.hdf tiltseries/VPP_tomo3.hdf tiltseries/VPP_tomo4.hdf tiltseries/mixedCTEM_tomo1.hdf tiltseries/mixedCTEM_tomo2.hdf tiltseries/mixedCTEM_tomo3.hdf tiltseries/mixedCTEM_tomo4.hdf --zeroid=-1 --tltstep=2.0 --npk=20 --tltkeep=0.9 --outsize=1k --niter=2,1,1,1 --notmp --pkkeep=0.9 --bxsz=32 --pk_mindist=-1 --threads=4

5) My computer has 4 GB RAM.

Thank you for your help.

Aditya

[Muyuan Chen]

1. Yes we updated the tutorial recently. The current tutorial is up-to-date with the current source code, which is a bit newer than 2.22. 

2. You should be able to use most functions described in the new tutorial in the 2.22 release, but 2.21a is a bit too old for this. I do not think e2tomogram works properly in 2.21a. Please consider update.

3. 4GB ram may be enough for the ribosome dataset, but is probably not enough for most tomogram processing...

Muyuan