Re: [scipion-users] import volumes with half maps question

[Pablo C. <pc...@cn...>]

Halves imported as halves will never be seen by the spyglass. The "main" 
volume will have the two halves associated "internally" and protocols in 
need of the halves will seek for this internal structure. Therefore 
providing the "main" volume will provide, at the same time the internal 
halves associated.

Now, if you want to treat any half as a volume to be chosen from any 
spyglass button, then you need to import it as a "main" map.

There might be a case where a protocol does not "expect" halves to be 
associated to a volume. Only in this case you'll need to import halves 
as main volumes. But we try to prevent this to reduce number of clicks 
and improve clarity as usability.

Cheers!

On 15/9/21 9:31, Lugmayr, Wolfgang wrote:
> Hi Marta,
>
> yes it worked, I did not expect to enter a file when the UI says "Files directory".
> Instead I tried to enter the file somehow in the "Pattern" input field.
> Maybe the help hints can be extended?
>
> Do I understand your description about half-maps attributes correctly?
> When I need to select 2 half-maps for e.g. ResMap FSC, I have to import them from the Relion job as single imports?
> Or is there a different way? In the spyglass selection box I cannot choose them, only the main map.
>
> Cheers,
> Wolfgang
>
>
> ----- Original Message -----
> From: "Marta Martinez" <mm...@cn...>
> To: "Mailing list for Scipion users" <sci...@li...>
> Sent: Tuesday, 14 September, 2021 19:23:31
> Subject: Re: [scipion-users] import volumes with half maps question
>
> Hi Wolfgang,
>
> I've tested the import volumes protocol and I've had no problems with
> SCIPION v3.0.9-Eugenius.
>
> I think that you can solve your problem filling in the "Files
> directory" with the path of the main map
> (/Runs/000500_ProtRelionRefine3D/extra/relion_class001.mrc) and then
> the "Path half map1" and "Path half map2" with the respective paths
> (/Runs/000500_ProtRelionRefine3D/extra/relion_half1_class001_unfil.mrc
> and
> /Runs/000500_ProtRelionRefine3D/extra/relion_half2_class001_unfil.mrc). I've
> tested this example and it works. ("Pattern" box is empty).
>
> However, the two half maps that you can import this way are not
> SCIPION objects, just the main map. The half maps are attributes of
> the main map and then they will not be recognized as maps by other
> protocols. So, if you want to use any of those half maps as input for
> a job in SCIPION I recommend you to import each one independently in
> an individual import volumes protocol writing its respective whole
> path in the box "Files directory". Sorry for the inconvenience.
>
> With best wishes: MARTA
>
>
> Quoting "Lugmayr, Wolfgang" <w.l...@uk...>:
>
>> Hi,
>>
>> I wanted to import 2 half-maps with the import volumes job.
>>
>> I selected the 2 maps with full path in the file browser and no
>> files directory or pattern:
>> When I press execute it says:
>> - The path and pattern can not be both empty!!!
>>
>> When I set also the files directory - error:
>> - Folders can not be selected.
>>    /home/lugmayr/foldername/
>>
>> When I set a file pattern + a files directory - error:
>> - You can not use the options 'Pattern' and 'Set half maps' simultaneously
>>
>> Do I miss something here?
>>
>> How do I select a half map from a relion refinement job as input for a job?
>>
>> Cheers,
>> Wolfgang
>>
>>
>> --
>> Universitätsklinikum Hamburg-Eppendorf (UKE)
>> @ Centre for Structral Systems Biology (CSSB)
>> @ Deutsches Elektronen-Synchrotron (DESY)
>> Notkestrasse 85 Gebäude 15
>> 22607 Hamburg, Germany
>> Tel.: +49 40 8998-87652
>> Email: wol...@cs...
>> http://www.cssb-hamburg.de/
>>
>>
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>
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*