Hello, everyone! I met a problem when I do the data processing of a small soluble protein. In the 2D Classification, I can see the clear secondary structure. However, When I do the abinitio and refinement( either homo or non-uniform), the map quality was strangely bad. It looked like there is some noise “wrapping” the protein. I guessed maybe the dynamic mask was too tight? But I remember the dynamic mask was very loose. So I didn’t understand what happened. I attempted many methods, such as:
- Ab-initio (12 A) - Homo Refinement - Non-Uniform Refinement
- Ab-initio (12 A) - Non-Uniform Refinement
- Ab-initio (6 A) - Homo Refinement - Non-Uniform Refinement
- Ab-initio (6 A) - Non-Uniform Refinement
- Or Ab-initio 4A…
All parameters of Homo Refinement or Non-Uniform Refinement were default.
There was a 2D picture of one refinement result. You can see the noise in the picture.
These refinement jobs worked well in many membrane proteins. However, I met this problem in the case. Can someone tell me the reason and some possible ways to resolve this?