[Pytom-mail] Particle extraction and pdb2em

[Kanika K. <kha...@gm...>]

Hello,

I am new to pytom and have the following questions:

1. pdb2em: I type in the following to convert my pdb file to em file:

pdb2em.py -p "pathtopdbfile" -s 4 -v 50 -o "pathtoemfile" and get the
following error message:
Traceback (most recent call last):
  File "/usr/local/pytom/bin/pdb2em.py", line 41, in <module>
    volume = pdb2em(pdbFile, float(pixelSize), int(cubeSize), chain =
chain,densityNegative = densityNegative)
  File "/usr/local/pytom/basic/files.py", line 369, in pdb2em
    return atomList2em(atomList,pixelSize,cubeSize,densityNegative)
  File "/usr/local/pytom/basic/files.py", line 297, in atomList2em
    centroidX = centroidX / len(atomList)
ZeroDivisionError: integer division or modulo by zero


Any ideas as to what might be wrong?

2. Once we have the localization file created as .xml and .sh file, how do
we get the scores.em and angles.em file for particle extraction? How to
visualize these files in chimera using the plugin mentioned in your website
(volumedialog_new.py)?

Thanks!

-- 
Best
Kanika Khanna
Graduate Student, Biological Sciences Department
University of California, San Diego