Problem while importing micrographs via e2helixboxer.py

[amanbi...@gmail.com]

Hello everyone,

I am a new user to EMAN2. I have installed software by following instructions from:

https://blake.bcm.edu/emanwiki/EMAN2/COMPILE_EMAN2_ANACONDA

on my mac version MAC OS 10.14.6   86_64

I am intend to calculate 2D class averages from the filamentous proteins. As I tried to use e2helixboxer.py command by giving path of the micrograph followed by e2helixboxer.py, however it is giving an error "Cannot execute binary file"

Any clue would be highly appreciable and helpful.

Thank you,

Kind regards,

Aman

[Steve Ludtke]

I think you may need to learn basic Unix/Mac command line usage. The command always goes first.

On Nov 2, 2020, at 12:44 PM, amanbi...@gmail.com <amanbi...@gmail.com> wrote:

Hello everyone,

I am a new user to EMAN2. I have installed software by following instructions from:

https://blake.bcm.edu/emanwiki/EMAN2/COMPILE_EMAN2_ANACONDA

on my mac version MAC OS 10.14.6   86_64

I am intend to calculate 2D class averages from the filamentous proteins. As I tried to use e2helixboxer.py command by giving path of the micrograph followed by e2helixboxer.py, however it is giving an error "Cannot execute binary file"

Any clue would be highly appreciable and helpful.

Thank you,

<Cannot_execute_binary_file.jpg>

Kind regards,

Aman

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<Cannot_execute_binary_file.jpg>

[Steve Ludtke]

Sorry, didn't mean to sound overly critical there. It was an honest suggestion. This is the sort of thing that most open-source software will assume the user is already familiar with. This is targeted at Linux, but most of the command-line principals and basic commands will be the same on a Mac:

https://ubuntu.com/tutorials/command-line-for-beginners#1-overview

[amanbi...@gmail.com]

Dear Prof. Steven,

Thank you for your feedback. First I had put command first as well. However, it wan not working either.

Sure, I am gonna work more on commands as I am a new user and look for possible problem.

Thank you,

Kind regards,

Aman

[Steve Ludtke]

Hi. I fear this is just the beginning of the learning curve. 

First, you need to make a "project folder", and cd into it before you start running programs like this. Otherwise you will clutter up your home directory with all sorts of files, which will only confuse you down the road.

Second, read this page:

http://eman2.org/Programs/e2helixboxer

and perhaps

e2helixboxer.py --help

I think that should get you started.

On Nov 2, 2020, at 5:59 PM, amanbi...@gmail.com <amanbi...@gmail.com> wrote:

Dear Prof. Steven,

Thank you for your feedback. First I had put command first as well. However, it wan not working either.

Sure, I am gonna work more on commands as I am a new user and look for possible problem.

Thank you,

Kind regards,<e2helixboxer.png>

Aman

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<e2helixboxer.png>

[Steve Ludtke]

You should probably also start with this:

https://blake.bcm.edu/emanwiki/EMAN2/Tutorials?action=AttachFile&do=view&target=EMAN2_GUITutorial.pdf

[amanbi...@gmail.com]

Dear Prof. Steven,

Thank you for the useful formation and links. Though particle picking of filaments by e2helixboxer.py is working now. As I had done similar analysis long time ago, but will brush basics again. 

Thank you,

Kind regards,

Aman