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?
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.
Thank you! I am going to use volume tool.