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

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

Forgot a "Hi Wolfgang!" or something similar. Now reading it looks rude. 
Extremely far from my intention and mood ;-) . Happy em processing!


On 15/9/21 10:53, Pablo Conesa wrote:
>
> 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/
>>>
>>>
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
> -- 
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*