Hi
I have attached an image of ribosome 3D model. This model is a complex of ribosome and 199-base long RNA. In the image you will see string of RNA is coming from the ribosome (if I am not overestimating) but when I look at the refined model, I don’t see any extra density for this RNA.
Is there any way to extract, refine particles with a bigger mask in order to see the extra density? OR any other way that you could kindly suggest to do focused classification , that will be highly appreciated.
when you say you don’t see it in the refined map, have you looked at the map filtered to low resolution? say 10-12Å? the region that you have circled looks very mobile
You are right, binding of RNA seems to be very transient. I have attached the image of refined map from two different angles. I only see little bit of RNA density allowing me to model only 10-12 bases. Also tRNA at P and A site are missing. When I did focused classification in relion I can see all 3 tRNAs at E, P, and A sites.
Could you please give me any suggestion how I can see more of it?
