I keep finding this area near my protein that looks like it means something but I’m not sure what to make of it. It was also apparent in the 2D classification stage with several classes. We’re expecting to see two proteins, so I am hoping that that’s the one? or an indication of what might have happened to it?
because although we had a complex of two proteins we can only see one so far in the volumes so I’m quite confused as to why it’s not there. Maybe it has unfolded near this area of our other protein? Im not sure how to make sense of it and would appreciate any insight.
What could I do to try and figure out what this is? I performed hetero refinement and am doing NU refinement for the good volume at the moment.
I get something similar with one of my proteins in a complex that has poor alignment and high mobility. You should give 3DVA a try, masking that region to see if it is maybe the protein you are looking for! Have you tried to low pass filter the map to see if you can see some features there at lower resolution?
Hi! Thank you for your reply. I’ll take a look at the guides of 3DVA. What do you mean by ‘masking that region’ though? Is there a way to tell cryosparc to put a mask over a certain area? and what would that achieve?
I’m also not sure what you meant by using a lowpass filter with the map. Is it a job on CS or is there anywhere I can read more about this or perhaps you can kindly elaborate on that?
Sorry about the plenty of questions but I’m still getting the hang of this and I haven’t gotten to this point before
