extraction of particle using e2helixboxer

[Nirakar Basnet]

Hi,

I am using e2helixboxer to extract particles form the micrograph.I have helix coordinates in .box file which is present in this format

1592 744 512 512 -3

Now I a trying to use this coordinates to extract the particle.

what i did was first import the helix coordinates using 

e2helixboxer.py --db-set-hcoords=001.box --helix-width=512  001.mrc

and then saved the particle using 

e2helixboxer.py 001.mrc --ptcl-length=512 --ptcl-width=512 --ptcl-overlap=452 --ptcl-norm-edge-mean --ptcl-not-rotated --ptcl-images-stack-mode --ptcl-images=001_ptcl.hdf

But the problem is o don't see any output file at all nor I see any error message?

Am I doing something wrong??

Thank you

Best Regards

Nirakar

[Steve Ludtke]

Hi Nirakar,

before we look in detail, please provide the complete output of e2version.py so we know exactly what you are using. It can have a significant impact.

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Steven Ludtke, Ph.D.

Professor, Dept of Biochemistry and Mol. Biol.         (www.bcm.edu/biochem)

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

Co-Director CIBR Center                          (www.bcm.edu/research/cibr)

Baylor College of Medicine                             

slu...@bcm.edu

[Nirakar Basnet]

Dear Steve,

here is the output of e2version.py

EMAN 2.12 (CVS 2015/10/19 09:00:04)
Your EMAN2 is running on:  Linux-3.0.101-94-default-x86_64-with-SuSE-11-x86_64 3.0.101-94-default x86_64
Your Python version is:  2.7.3

thank you

Beast Regards

Nirakar

[Steven Ludtke]

Hi Nirakar,

sorry for the very slow response on this. Overwhelmed with deadlines. I just did a quick test (with 2.2). First I ran:

e2helixboxer micrographs/*mrc --gui

and went through the process that way, including saving particles and coordinates, and everything worked properly. Then I did:

e2helixboxer.py micrographs/BGal_000021.hdf --ptcl-images BGal_000021_ptcl.hdf --helix-width 128 --ptcl-overlap 64

and this also produced the expected particle output files. This makes me think that there may be an issue with the version you have?  I know there was a period during which we were transitioning from the old-style BDB: files (EMAN2.0) to HDF files (EMAN2.1+) with JSON metadata, and have a vague memory that someone had forgotten to update e2helixboxer at some point.

Anyway, I would suggest downloading 2.2 and giving it a try if you haven't already solved the problem