Can local refined map be combined with the original map?

Hi, all

I am just started to use the local refinement job trying to improve the resolution of one of the domains of the protein.
But I don’t know what to do after obtaining the map generated by local refinement.
Can I combine it with the original one so that the map region of this domain can be replaced by the local refined map?
Or can I only use it separately in model building?
Then what about the model validation?
Should I do individual validation?
Sorry about these newbie questions.

Also, I am wondering is there any difference between the " Local Refinement" job and "NU Refinement with the mask covering the region to refine " ?


Update:
One of my local refinement (New) job completed and I found it a complete reconstruction of my protein rather just a sub-volume covered by the local mask.
So I don’t have combine the maps and can treat it as a full construction for the following model building and validation?

Jessica

Local refinement will only search and improve euler angles close to what are already assigned (user input typically 20Å shift 10°rotation I think), whereas global refinement with mask will completely reassign euler angles taking into account only the information within the mask.

Maps can be combined for figure making with chimera vop maximum. Or you can use reconstruction to generate the whole particle using assignments from local refinement, but this will make the other regions uninterpretable I’m sure. I look forward to more info about model building and independent validation - so far my plan is to build into higher-res local maps and then use these models for map/model validation of the lower res whole particle. I will certainly upload the sub-volume as well, as an independent map.

@CryoEM1

Thanks for your reply.
Got it.
So I can use vop maximum to generate a higher resolution map to support model building. Then using the lower resolution original map for validation and upload both maps.
Do I also need to provide the validation number of the whole combined map?
Or just validate with the the original map and the sub-volume?

Jessica

Hello,

If I may add, I would first filter local maps with soft masks with vop multiply, then run vop maximum to generate a combined map. This way, noise signal in local maps outside masks won’t contribute to the resulting combined map.

As mentioned, I would build models into higher-res local maps, then use the combined map and the final model for model validation. In a figure, I would include FSC curves of all local maps including the FSC curve for the lower-res global map.

Lastly for map deposition, I would upload:

  1. combined map
  2. global reconstruction and half-maps
  3. local maps and their half-maps

Best,
Kookjoo

thanks kookjoo, this is great info. @jessho as for the update above, that is very unusual and likely means you did not correctly use a mask for the job. I would double check that the mask you are using is a sub-volume (if that’s what you are interested in focusing on) and then the result should be a sub-volume.

Thanks. I am very appreciated for the useful and clear info.

All the best,
Jessica

@CryoEM1

I am sure my mask is a sub-volume.
When I used the same mask for both NU and local refinement job, the resulting volume in NU is a sub-volume; however, for the local refinement job, the volume displayed by Chimera is a full reconstitution of my protein.
But when I using the local resolution estimation, the value of the regions beyond the mask is 0. So it seems not to be existed.