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

[Lugmayr, W. <w.l...@uk...>]

Hi Pablo, 

thank you and no worries, I prefer the solution part of your answers ;-) 

I just wanted for curiosity compare the results of fsc3d, bsoft blocres and resmap. 
the later two accept only real half-maps in their form. 

I will try. 

Cheers, 
Wolfgang 



From: "Pablo Conesa" <pc...@cn...> 
To: "Mailing list for Scipion users" <sci...@li...> 
Sent: Wednesday, 15 September, 2021 11:12:11 
Subject: Re: [scipion-users] import volumes with half maps question 



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: 

BQ_BEGIN

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" [ mailto:mm...@cn... | <mm...@cn...> ] To: "Mailing list for Scipion users" [ mailto:sci...@li... | <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" [ mailto:w.l...@uk... | <w.l...@uk...> ] : 

BQ_BEGIN

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


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BQ_END

-- 
Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team 


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