Re: [Pytom-mail] converting particlelists into motivelists

[Ortiz, J. O. <or...@bi...>]

Dear Emmanuel,
I found in my records, some matlab procedures that I wrote exactly for your purpose, but I can not garantee that they are working with your list. I would start with the version 3 (_v3.m) which should be the latest.
Sorry for not given you more details. Since a while I don't use these tools.
Saludos,
Julio
________________________________
Von: Emmanuel Moebel [emm...@in...]
Gesendet: Donnerstag, 30. März 2017 16:37
An: pyt...@li...
Betreff: [Pytom-mail] converting particlelists into motivelists

Dear Pytom community,

I would like to convert particle lists (.xml file) produced by pytom into "motive lists" (.em file), as used in the matlab TOM and AV3 toolboxes (see https://www.biochem.mpg.de/tom ).
I started writing a pytom script in order to do that:

--------------------------------------------------------------------

from pytom.basic.structures import ParticleList

partlFile = 'aligned_pl_iter9.xml'
motlFile = 'motl_aligned_iter9.em'

pl = ParticleList()
pl.fromXMLFile(partlFile) # read particle list

pl.toMOTL(motlFile) # save as motive list

--------------------------------------------------------------------


This script transfers most informations from the particle list into the motive list, except for the particle IDs, which is annoying.

In the motive list row where should be the particle IDs, I just have 0,1,2,3,4,5 .... But this IDs don't correspond to the particle infos (position, orientation etc)


Is there something I missed? Or maybe someone already wrote a script and is willing to share it?


Best regards,

Emmanuel Moebel

PhD student at Inria Rennes (France)

Member of team Serpico