Re: [scipion-users] exporting an EMX file to cryoSparc

[Juha H. <ju...@st...>]

Hi Jose Miguel

First I tried exporting a setOfParticles, saved from a 3D classification
(all particles from one class), to an EMX file. After importing back to
Scipion (choosing alignment type Projection), this produced a smooth blob.
Next I tried the same, but from a 3D refinement that I had run on the same
set of particles. This worked just fine.  So is the alignment information
stored / exported somehow differently for setOfParticles object in these
two cases?

CryoSparc was not working even now so I will ask the developers.

Best wishes,
Juha

On Sat, Mar 4, 2017 at 10:03 AM, Jose Miguel de la Rosa Trevin <
del...@gm...> wrote:

> Hi Juha,
>
> Thanks for your feedback. Could you do a small experiment to detect if the
> exported EMX file is correct? Could you import back the EMX file into
> Scipion and try to reconstruct only with Relion (there is a protocol for
> that) and check if it makes sense or not. Take into account that the map
> probably will not be exactly the same that originally came out from Relion,
> since it is filtered.
>
> Anyway we will also check about this issue.
>
> Bests,
> Jose Miguel
>
>
> On Fri, Mar 3, 2017 at 9:46 AM, Juha Huiskonen <ju...@st...>
> wrote:
>
>> Hello
>>
>> I was wondering if the EMX export should work and if others have managed
>> to use it with cryoSparc?
>>
>> I exported my dataset and imported EMX files to cryoSPARC after running
>> Relion 3D refinement through Scipion. Import to CryoSparc seemed to work
>> (it created a gallery of the images) but results from the first ab initio
>> run were nonsensical.
>>
>> Next I tested importing MRC files and a corresponding STAR file (manually
>> converting the same particle stacks to MRC and providing them together with
>> a corresponding Relion STAR file from the refinement run). After the same
>> run in cryoSparc, the results were as expected.
>>
>> Any ideas? Apologies if this is likely to be an issue on the cryoSPARC
>> side, in this case I would  naturally contact those developers.
>>
>> Best wishes,
>> Juha
>>
>>
>>
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