The beam tilt parameters cannot be determined easily from the data. They should remain constant throughout a microscope session, however. If you do not know them you could perform a search in which you recalculate the reconstruction for a number of different beam tilt parameters and see which one yields the best reconstruction. A grid search with steps of 0.01 and a range of - 0.03 to 0.03 in both directions would be a good start.
So it is more mathmatic optimization than real beam tilt, right? I dont know what is the unit of beam tilt here. But it seems not a small value in real microscope.
So when we should do this kind of optimization? Now we have Ewald correction, defocus correction, astigmatism correction, beam tilt correction, even mag correction, what is the order to do them?
At 4 A resolution you should be able to see a lot of the larger side chains. This should give you some idea about the quality of the map. To get a quantitative measure, you could build a model and calculate a correlation coefficient.
What do you mean by "the best reconstruction"? I always have this question. As a crystallographer we normally use Rfree to be a reference. Whe we turn on some parameters to refine and Rfree go up, than we know we should turn it off. But is there a clear standard to test that we know it is good to go or stop?
The beam tilt parameters
The beam tilt parameters cannot be determined easily from the data. They should remain constant throughout a microscope session, however. If you do not know them you could perform a search in which you recalculate the reconstruction for a number of different beam tilt parameters and see which one yields the best reconstruction. A grid search with steps of 0.01 and a range of - 0.03 to 0.03 in both directions would be a good start.
Is it only mathmatic
In reply to The beam tilt parameters by niko
So it is more mathmatic optimization than real beam tilt, right? I dont know what is the unit of beam tilt here. But it seems not a small value in real microscope.
So when we should do this kind of optimization? Now we have Ewald correction, defocus correction, astigmatism correction, beam tilt correction, even mag correction, what is the order to do them?
What resolution are you
In reply to Is it only mathmatic by mbycliaw
What resolution are you working at?
High resolution
In reply to What resolution are you by niko
Assume it is a high resolution one, say 4A.
At 4 A resolution you should
In reply to High resolution by mbycliaw
At 4 A resolution you should be able to see a lot of the larger side chains. This should give you some idea about the quality of the map. To get a quantitative measure, you could build a model and calculate a correlation coefficient.
what is the best reconstruction
In reply to The beam tilt parameters by niko
What do you mean by "the best reconstruction"? I always have this question. As a crystallographer we normally use Rfree to be a reference. Whe we turn on some parameters to refine and Rfree go up, than we know we should turn it off. But is there a clear standard to test that we know it is good to go or stop?