How to combine two local-refined maps of two parts from one protein into one map in Cryosparc?

Local Refinement
1

Hi, all,

I manully seperated my protein into four parts and locally refined each by using the subtracted particles and it indeed give us some better results. However, this will lead to recenter each part at the center of box, since the defined fulcrum setting. Now I want to combine four local-refined maps into one map for modelling. Could you tell me whether it is possible or not? How to handle this in Cryosparc or any others?

thanks!

Niu

1 Like
2

Hi,

In the “new” local refinement in 3.1, each part remains in its original location - not recentered in the middle of the box. This makes map combination and other downstream operations such as particle subtraction more convenient.

For map combination, aligning maps to a global reconstruction and combining by taking the maximum value at each voxel (vop maximum in UCSF Chimera) is the best method I have found to get a seamless combination. I would still encourage deposition of the orginal component maps as well, though.

Cheers
Oli

5 Likes
3

Hi @niu,

Seconded Oli’s suggestions. Using the new version should preserve the original orientations and positions of each body/mask, making it easier to combine maps using the procedure Oli mentioned. I don’t know too much about what the EMDB standards are, but it appears that individual body maps are routinely uploaded (e.g. see entry 21105, from a RELION multibody refinement).

Best,
Michael

4

Thanks for your quick reply. I will try the “new” local refinement later. Also, I agree with you to deposite the orginal maps in the final state. Here actually, the combinated map is just used for modelling the initial structure more easily at the beginning.

5

Thanks a lot. Maybe Relion multibody refinement is another choice and I can have a try later.