Local resolution colored map with composite maps

[Bassem]

@HaoweiZhang is it possible to make a local resolution colored map with composite maps?

[mmclean]

Hi @Bassem,

It is only possible to do this right now in external software. If you have two local refinements in the same reference frame (i.e. no particle origin shifting has been done in Volume Alignment Tools, for example), you might be able to follow a similar path to the quoted reply below. That is, you could take the maximum local resolution value between each of the local resolution maps, for each voxel in the map. The local resolution maps output their results in Angstroms (not inverse Angstroms), so you would want to use the minimum value in this case. This could be done with the vop minimum command in UCSF Chimera.

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

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 comp…

I would encourage you to review some previous discussions on the forum before proceeding with this, as some users (see above) have recommended to keep the distinct maps (and hence their local resolution maps) separate when depositing. You may also find this thread helpful: Can local refined map be combined with the original map?

Best,
Michael

[Bassem]

thanks @mmclean. We had a long single loop domain that was refined differently across two sub volumes and given its nature it is spotty and lower resolution than the rest of the map so having its resolution across the composite map would have been great. i will look into the resources you shared. thank you

[Bassem]

Just to add. i was able to carry it out in Phenix by submitting half maps for each local refine map and do the alignment in phenix. it produced two half maps and the composite maps (vs chimera which will produce only the composite map).