Zhanglab forum

I am a new user to EM-refiner, so I apologize if my queries are dumb

I am confused by what is meant by 'sampling rate' in the command needed to run the program. If you could kindly clarify, that would be great!

Also, In the readme text of the downloaded software package, the sampling rate is mentioned as '5.0 0.0'. Can this value be used for any structure refinement? If it needs to be changed, what would be the basis for it? Thank you!

Hello,

sampling rate is downsampling rate for the density map. it is used to speed up the refinement, but will reduce the accuracy of the refinement. We don't use it in the program. 0.0 means we don't do downsampling in the program.

Thanks,
Biao

Hello,

Thank you for your response! I will be using it as 0.0 0.0 in future refinement.

Since you mentioned about the speed of the refinement, I have a follow-up question. Does the method use parallel processing on multiple CPU’s, or one CPU? Thank you!

Hello,

'5.0 0.0' is two different parameters, 5.0 is the resolution of density map that you use in the program. the resolution should be change according to the density map. 0.0 is unsampling rate that it don't need to change in the program.
By the way, we haven't developed a parallel version.

Thanks,
Biao