Re: [Pytom-mail] Imposing D4 symmetry?

[Ricardo R. <ric...@gm...>]

Thanks Dustin!

I have tried it, but then I get this error:

Traceback (most recent call last):
  File "/fs/pool/pool-bmapps/hpcl8/app/soft/PYTOM/0.97/pytom/bin/align.py",
line 45, in <module>
    exj.fromXMLFile(jobFile)
  File
"/fs/pool/pool-bmapps/hpcl8/app/soft/PYTOM/0.97/pytom/basic/structures.py",
line 74, in fromXMLFile
    self.fromStr(lines)
  File
"/fs/pool/pool-bmapps/hpcl8/app/soft/PYTOM/0.97/pytom/basic/structures.py",
line 47, in fromStr
    self.fromXML(root)
  File
"/fs/pool/pool-bmapps/hpcl8/app/soft/PYTOM/0.97/pytom/alignment/ExMaxAlignment.py",
line 275, in fromXML
    self._symmetry  = symmetryFactory.fromXML(symmetryXML[0])
IndexError: list index out of range

I see there is indeed a MultiSymmetries class that expects an XML
description of symmetries, but I could not find the specification of such a
file.

>From the example in the documentation, it seems that only Cn symmetries are
supported in this kind of job?

<Symmetry X="0.0" Z2="0.0" NFold="1"/>*<!-- Symmetry information (C-X)
supported currently)*
http://strubi.chem.uu.nl/pytom/doc/pytom/RealSpaceExMax.html

--
Ricardo Diogo Righetto


Em ter., 30 de mar. de 2021 às 15:26, Dustin Morado <dus...@gm...>
escreveu:

> Hi Ricardo,
>
> Did you have the symmetries wrapped in a multi-symmetry object? It should
> look something like this:
>
> <MultiSymmetries>
>   <Symmetry NFold="4" SearchAngle="0" SearchAxisX="0.0" SearchAxisZ2="0.0" Type="PointSymmetry" X="0.0" Z2="0.0"/>
>   <Symmetry NFold="4" SearchAngle="0" SearchAxisX="0.0" SearchAxisZ2="0.0" Type="PointSymmetry" X="180.0" Z2="90.0"/>
> </MultiSymmetries>
>
> Cheers,
>
> Dustin
>
>
> On Tue, 30 Mar 2021 at 14:06, Ricardo Righetto <ric...@gm...>
> wrote:
>
>> Hi,
>>
>> For imposing C4 symmetry in a real space alignment job, I use the
>> following tag in the job XML file:
>>
>> <Symmetry NFold="4" SearchAngle="0" SearchAxisX="0.0" SearchAxisZ2="0.0"
>> Type="PointSymmetry" X="0.0" Z2="0.0"/>
>>
>> But how would I go about imposing D4 symmetry? I tried adding another
>> line to describe an additional 2-fold axis rotated by the 90 degrees, but
>> it is ignored and only the C4 is imposed...
>>
>> Thanks!
>>
>> --
>> Ricardo Diogo Righetto
>> _______________________________________________
>> Pytom-mail mailing list
>> Pyt...@li...
>> https://lists.sourceforge.net/lists/listinfo/pytom-mail
>>
>