Hi,
I have been playing around with Bayesian polishing in relion 3, and it has already been extremely helpful - up to 0.5 Å improvement in one case.
I am now trying to apply it to some other, more challenging cases, and I have a couple of queries that I’m hoping someone more knowledgeable might be able to help out with:
1. I have a dataset from a symmetric protein that is asymmetrically disposed within a nanodisc. In such a case, I get better resolution during refinement by enforcing symmetry, but if I understand correctly the important thing during bayesian polishing is comparison of the projection of the reference map with the aligned particle image. In such a case would I be better using a C1 refinement to start Bayesian polishing, even if it is somewhat lower in resolution?
2. I would like to start polishing from orientations obtained in another package (cryoSPARC in this case). I am assuming that the polishing algorithm is expecting a map that has been calculated in relion, but in certain cases I obtain substantially better resolution in cryoSPARC. In this case, could I just take the cryosparc orientations, calculate two half maps using relion reconstruct, and then use relion_postprocess on those half maps? Or does the refinement itself need to be performed in relion?
3. How important is the training to the final outcome? The optimal parameters for each dataset reported in the preprint are dramatically different. For small, low SNR particles, should we be using more particle images in the training step for optimal results?
4. Not related to Bayesian polishing, but concerning CtfRefine - I have tried this for large particles and got excellent results, but haven’t had the same success with small particles - the datasets I’ve tried so far have given a very large range of per particle defoci with a drop in resolution in refinement afterwards - any tips would be most welcome!
Cheers
Oli
(PS thanks so much for this amazing new set of tools!)
########################################################################
To unsubscribe from the CCPEM list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
|