Extracting replicating unit from map

Model Building
1

Hi All,

I am working with two cryo-EM maps of completely unknown proteins: one reconstructed with I symmetry (virus head, T=7 levo) and another with C6 symmetry. For model building, I would like to isolate a single asymmetric unit (ASU) / repeating unit from each map, which should make the process of model building more manageable.

Could anyone kindly suggest the best approaches or tools to extract one ASU from these maps?

Thanks in advance for your help.

2

After you have fit a model of your protomer, you can use phenix.map_box for this: phenix.map_box: extract box with model and map around selected atoms

2 Likes
3

Thanks for the reply. Definitely with a model it will be much easier to identify with variety of methods. I don’t have a model. There is no known structure. Is there a way I can identify the repeating unit without the model?

4

A brute force approach would be to crop the volume down in Chimera so that it’s one semi-hemisphere, then feed it to Model-Angelo with build_no_seq and see if you can see a repeating pattern in the modelled chains. Then select them, export and follow the suggestion for phenix. :slight_smile:

Or just feed the whole volume to Model-Angelo with build_no_seq if it’s not too big and/or your GPUs have a lot of VRAM. If handedness is correct you should have a pretty good capsid model out the other side, and if not, z-flip the map and try again. Then identification of an ASU should be fairly easy.

3 Likes
5

Ah yes that’s trickier. Scipion/xmipp apparently has a way but haven’t tried it…

https://scipion-em.github.io/docs/release-3.0.0/docs/user/tutorials/modelBuilding/Homology/a070-extractUnitCell.html