I have got the mirror map of the structure

Model Building
1

I have got a map related to a protein using CryoSparc. This protein already has several published structures. When I tried to fit one of these structures into the map, it couldn’t be aligned and it seems that the map is in the mirror state of the protein. I have used C1 for my Ab-initio and I don’t understand how it has happed. I tried to repeat the process but it gave me the same results. Can anyone help me in this matter?

2

This is normal.

Using any ab initio method, you have an equal chance of converging on the correct or inverted hand.

If you think about this on a per particle level this makes sense - your particles are ~2D projections of the 3D structure(s), so you cannot tell chirality (a top view of a right hand looks the same as the bottom view of a left hand).

You can just flip the map (using Volume Tools, or vop zflip in UCSF Chimera, for example) and you should be good to go.

Cheers
Oli

2 Likes
3

Thank you! I am going to use volume tool.

4

Hi Oli,

Thank you for your input, it is very helpful.
I have a follow-up question regarding this thread - how would you handle the case where the ab initio reconstruction classifies mirrored particles into two classes? Should I rerun ab initio with fewer classes?

Thank you,
Jiarui

5

If you can determine which is the correct hand, just take that model and move forward with that one, using the particles from both.

1 Like
6

Thank you for the clarification!