Re: [Pytom-mail] converting particlelists into motivelists

[Thomas H. <th...@gm...>]

Hi Emanuel,

Yes, the documentation of toMOTL states that the result may not be consistent with the particle index, it enumerates the index from 1:numberParticles.

http://pytom.org/doc/epydoc/index.html <http://pytom.org/doc/epydoc/index.html>

However, you can copy your files into a new folder with 
copyFiles(self, destinationDirectory, particlePrefix)

and this way the new particles would be consistent to a new MOTL list.

Hope it helps,
Thomas

> On Mar 30, 2017, at 7:37 AM, Emmanuel Moebel <emm...@in...> wrote:
> 
> 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 <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
> ------------------------------------------------------------------------------
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