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

[Jose M. de la R. T. <del...@gm...>]

Hi Juha,

The angular assignment information in a 3D classification and 3D refinement
should be similar, with the main difference that the former could be
associated to many classes. I will check this problem, because, as you
expected, exporting on 3D class assigned particles should produce a volume
similar to the class representative 3D structure.

Please let us know about any news from CryoSparc developers regarding the
EMX import.

Bests,
Jose Miguel.


On Wed, Mar 8, 2017 at 3:28 PM, Juha Huiskonen <ju...@st...> wrote:

> 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
>>>
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
>>>
>>
>