Re: [Pytom-mail] Imposing D4 symmetry?

[Dustin M. <dus...@gm...>]

Hi Ricardo,

I remember this now, I had written my own alignment scripts and was doing
icosahedral symmetry, and I know that was working, so I will do some
digging and try to send you the patch for making multisym work.

Cheers,
Dustin

On Tue, 30 Mar 2021 at 17:26, Ricardo Righetto <ric...@gm...>
wrote:

> 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
>>> _______________________________________________
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>>