skip orientation refinement, only reconstruct refinement.db

[Ryan Casner]

Hello,

I was wondering if there is any way for segmentrefine3d to only do the reconstruction of a prior refinement.db, bypassing the orientation refinement.  I have had very good results with spring and believe my orientations have converged, and now I would like try to save some time trying to refine my other parameters (including/excluding segments, b-factor, etc.)

Thanks,

Ryan Casner

Conway Lab

University of Pittsburgh Structural Biology

[Carsten Sachse]

Hi Ryan,

Yes, you can skip any orientation search but rely on the existing parameters for the 3d reconstruction. You have to specify:

Number of iterations                     = 1

Reference structure option               = False

Continue refinement option               = True

refinement.db file                       = your_refinement.db

This will generate another 3d reconstruction with the parameters as determined in your_refinement.db

This way, you can test the effect of different exclusion criteria. It is not recommended to play with B-factor, this will only affect the alignment and should only be applied if you have a good reason to do it. Under normal circumstances, it has the danger of overfitting the high-resolution terms during alignment.

Best wishes,

Carsten

[Ryan Casner]

Ahh, I see now.. Thanks for your help!