eman2 old particle picker

[Abdul Basit Khan]

dear all,

   I am trying to process negative stained TEM data for envelope generation.

I have converted .tif images to micrographs in .hdf format.. As per the tutorial i have to picke particle by "old particle picker". so there should be a browsing option select all micrographs and put box size and the launch...but i am not able to see that on my GUI.

Please help me with that.

[Steve Ludtke]

Hi. Which tutorial are you following?  I think the deep learning picker should be fine with negative stain data, but can't say I've tried it recently.  For us to help, we need:

1) URL of the tutorial you're using

2) full output of e2version.py on the machine where you're running EMAN2

3) when something fails in the GUI, very often an error message will be printed in the console window where you launched e2projectmanager.py from. The full text of any such errors would help a lot.

4) Any project details you're willing to share publicly, primarily the A/pix of your images and the size and symmetry of the targeted particles

cheers

--
--
----------------------------------------------------------------------------------------------
You received this message because you are subscribed to the Google
Groups "EMAN2" group.
To post to this group, send email to em...@googlegroups.com
To unsubscribe from this group, send email to eman2+un...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/eman2

---
You received this message because you are subscribed to the Google Groups "EMAN2" group.
To unsubscribe from this group and stop receiving emails from it, send an email to eman2+un...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/eman2/cf4f6f8b-29fd-4f63-aea1-a76cd3bfb103n%40googlegroups.com.

[Abdul Basit Khan]

thanks for your reply

1. https://indico4.twgrid.org/event/4/contributions/635/attachments/360/415/EMAN2_ISGC_tutorial_20180321.pdf ; this is the tutorial i am working with.

2. it's EMAN 2.9 PROJECT MANAGER ; i have generated micrographs in .hdf format .

3. there is no error message on the screen. just it doesn't show any browsing window unlike other options.

4. yes i'll share the other informations soon

[Abdul Basit Khan]

On Friday, January 30, 2026 at 5:01:52 AM UTC+5:30 Steve Ludtke wrote:

[Steve Ludtke]

Hi Abdul,

the official documentation, including tutorials on several different topics are located at 

http://eman2.org

Specifically, I'd start with:

- NegativeStain

- Quick Introduction to the EMAN2 GUI 

- Single particle analysis tutorial

For question 2, you need to go to the terminal and run "e2version.py" and provide the complete output. "EMAN2.9" isn't specific enough to be useful. Specific versions may have had specific bugs.

For question 3, it's important that you're checking the terminal window for the error messages. A few "normal" errors will produce pop up error messages on the screen, but less common errors will just be printed in the terminal, which is often not visible when you have the GUI open unless you bring it to the front.

To view this discussion visit https://groups.google.com/d/msgid/eman2/126da607-d33d-41c7-be53-96525ebf2c2an%40googlegroups.com.